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The regulation of COX-2, ABCA1 and ABCG1 by the lncRNA PACERR links the inflammatory response and cholesterol homeostasis

GSE328984 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/07/20 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 18 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
18 samples: 6 conditions, mostly in triplicateGroups 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)
The COX-2 antisense lncRNA PACERR interacts with discrete RNA binding proteins to mediate a cell specific COX-2 response to HDL. PACERR exerts its action both in cis and in trans, controlling the expression of COX-2 in macrophages, while also regulating the levels of macrophage ABCA1 and ABCG1, cholesterol transport genes involved in maintaining cholesterol homeostasis.
Read the full summary ↓
When cells are exposed to HDL, PACERR is transcribed, leading to the release of bound histone acetyltransferase p300 and its relocation to the promoter of COX-2 which is then transcribed, leading to PG formation. In concert, PACERR also releases heterogeneous nuclear ribonucleoprotein L (hnRNPL) which relocates to the ABCA1 and ABCG1 gene loci, controlling mRNA alternative splicing and subsequent cholesterol efflux to HDL. A strong hnRNPL binding site motif is found in PACERR RNA and when this was deleted, the interaction between PACERR RNA and hnRNPL is abrogated both at baseline and following HDL treatment of macrophages. THP-1 macrophages stably overexpressing PACERR (P1-3) or deleted of the hnRNPL binding site (Delta1-3) from the PACERR sequence. In delta cells, PACERR no longer binds to hnRNPL but is free to bind to ABCA1 and ABCG1 impacting their transcription. In summary, we found that PACERR controls the levels of the cholesterol transporters through its interaction with the splicing factor, hnRNPL. It is released from PACERR RNA in response to HDL where it relocates to introns of cholesterol transporters determining the alternative splicing fate of transcripts required for cholesterol efflux. Through use of the delta cells, we have Illustrated the specificity for the interaction between hnRNPL and PACERR.
This dataset
Open GSE328984 in finder → Find more human 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 GSE328984_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1457316 and SRA study SRP694466. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
Empty vector, untreated, ×3 Empty vector, HDL treated, ×3 PACERR overexpression, untreated, ×3 PACERR overexpression, HDL treated, ×3 PACERR overexpression with hnRNPL motif delet… ×3 PACERR overexpression with hnRNPL motif delet… ×3

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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
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