← BioTransfer GEO Dataset Finder
GEO series

Induced Expression of VEGFC, ANGPT, and EFNB2 and Their Receptors Characterizes Neovascularization in Proliferative Diabetic Retinopathy

GSE102485 Homo sapiens (human) RNA-seq (gene expression) 30 samples Submitted 2020/08/10 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 30 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
30 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)
Proliferative diabetic retinopathy (PDR) is the advanced stage of diabetic retinopathy (DR), coupling with irregular neovascularization, and is the leading cause of blindness in working-age people; but the molecular mechanism of vascular differentiation in PDR remains poorly characterized. In our study, we obtained the transcriptome profile of neovascular proliferative membrane specimens from patients with PDR via high-throughput sequencing and advanced bioinformatics.
Read the full summary ↓
Marker genes of neovascularization were validated and distinct gene expression patterns were formed of PDR compared with normal retina. We also discovered gene sets that were co-expressed with vascular endothelial growth factor A (VEGFA), including transcription factors (TFs) that dysregulate VEGFA. In particular, ETS transcription factors family could negatively regulate VEGFA. We also detected a set of genes related to PDR was dramatically changed from pre-mRNA to mature mRNA. In summary, our study firstly presented the profile of neovascular proliferative membrane and identified new marker genes and key regulators of VEGFA, which could contribute the molecular therapy of PDR in the future.
This dataset
Open GSE102485 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 GSE102485_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 PRJNA397857 and SRA study SRP115195. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 31574534) ↗
Samples in this study

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

+ 30 more — browse all 30 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq 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.