GEO series

MicroRNAs are Transported in Plasma and Delivered to Recipient Cells by High-Density Lipoproteins (HG-U133 2.0)

GSE25311 Homo sapiens (human) Expression microarray 6 samples Submitted 2011/03/24 Platform GPL570

At a glance

Expression microarray · human · 6 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 6 samples: 3 × Huh7 cells treated with Normal HDL, vs 3 × Huh7 cells treated with FH HDL,Groups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Circulating microRNAs (miRNA) are relatively stable in plasma and are a new class of disease biomarkers. Here we present evidence that human high-density lipoprotein (HDL) transports endogenous miRNAs and delivers them to recipient cells with functional targeting capabilities. Highly-purified fractions of human HDL contain small RNAs, and the HDL-miRNA profile from normal subjects is significantly different than familial hypercholesterolemia subjects.

Read the full summary ↓

miRNAs were demonstrated to associate with both native and reconstituted HDL particles, and reconstituted HDL injected into mice retrieved distinct miRNA profiles from normal and atherogenic models. Cellular export of miRNAs to HDL was demonstrated to be regulated by neutral sphingomyelinase. HDL-mediated delivery of miRNAs to recipient cells was demonstrated to be scavenger receptor BI-dependent. Furthermore, HDL delivery of both exogenous and endogenous miRNAs resulted in the direct targeting of mRNA reporters. Notably, HDL-miRNA from atherosclerotic subjects induced differential gene expression, with significant loss of conserved mRNA targets in cultured hepatocytes. Collectively, these observations suggest that HDL participates in a novel mechanism of intercellular communication involving the transport and delivery of miRNAs. Gene expression changes in human Huh7 cells with familial hypercholesterolemia HDL treatment.

This dataset

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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 (GSE25311_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 ↓

What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA142557. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21423178) ↗

Study design

3 × Huh7 cells treated with Normal HDL, vs 3 × Huh7 cells treated with FH HDL,

Supports a between-group comparison across 6 samples.

How we read this: 2 replicated groups read from 6 sample titles; they account for 6 of them. 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

GSM622576 Huh7 cells treated with Normal HDL, biological rep 1 Huh7 cells treated with…
GSM622577 Huh7 cells treated with Normal HDL, biological rep 2 Huh7 cells treated with…
GSM622578 Huh7 cells treated with Normal HDL, biological rep 3 Huh7 cells treated with…
GSM622579 Huh7 cells treated with FH HDL, biological rep 1 Huh7 cells treated with…
GSM622580 Huh7 cells treated with FH HDL, biological rep 2 Huh7 cells treated with…
GSM622581 Huh7 cells treated with FH HDL, biological rep 3 Huh7 cells treated with…

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