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Injury response of human lens epithelial cells ex-vivo

GSE186716 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/10/27 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 12 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
12 samples: 3 × Cortical fiber cells, vs 3 × Equatorial lens epithelial cells, 0 hours post injury vs 3 × Equatorial lens epithelial cells, 24 hours post injury vs 3 × Central lens epithelial cells,Groups 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.
Paper
Human lens epithelial cells induce the inflammatory response when placed into the lens capsular bag model of posterior capsular opacificationMolecular vision · 2024
Summary (written by the submitters)
This study investigates the response of human lens epithelial cells to mechanical injury. Human geriatric lenses obtained from cadaver eyes from donated to an eye bank for research were subject to in-vitro capsulotomy mimicking the injury sustained during cataract surgery. The anterior capsule was dissected using a curvilinear capsulorhexis technique, and central lens epithelial cells attached to the patch of anterior capsule (Rhexis) were immediately stabilized in RNAlater.
Read the full summary ↓
The fiber cells were then removed, and the cortical fibers were immediately stabilized in RNA later. The remaining equatorial lens epithelial cells attached to the capsular bag from one eye were stabilized in RNA later immediately while the equatorial lens epithelial cells from the other eye were cultured for 24 hours then stabilized in RNAlater.
Published in
Human lens epithelial cells induce the inflammatory response when placed into the lens capsular bag model of posterior capsular opacification
Novo SG, Faranda AP, D'Antin JC et al. · Molecular vision 2024 · PMID 39959166
This dataset
Open GSE186716 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 GSE186716_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 PRJNA775637 and SRA study SRP343478. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39959166) ↗
Study design
3 × Cortical fiber cells, vs 3 × Equatorial lens epithelial cells, 0 hours post injury vs 3 × Equatorial lens epithelial cells, 24 hours post injury vs 3 × Central lens epithelial cells,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

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