Patient-derived cornea organoids as drug repurposing models for aniridia-associated keratopathy
RNA-seq (gene expression) · human · 9 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
- 9 samples: 2 × AAK_iPSC_S vs 2 × WT_Control_D vs 2 × AAK_D30_S vs 2 × AAK_D90_SGroups 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.
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE307222_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1314783. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 9 sample titles; they account for 8 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.
- GSM9219374 control_ipsc
- GSM9219375 AAK_iPSC_S1 AAK_iPSC_S
- GSM9219376 AAK_iPSC_S2 AAK_iPSC_S
- GSM9219377 WT_Control_D30 WT_Control_D
- GSM9219378 AAK_D30_S1 AAK_D30_S
- GSM9219379 AAK_D30_S2 AAK_D30_S
- GSM9219380 WT_Control_D90 WT_Control_D
- GSM9219381 AAK_D90_S1 AAK_D90_S
- GSM9219382 AAK_D90_S2 AAK_D90_S
- GSE288179 Differential response of patient-derived intestinal organoids to site-specific mucosal bacteria in pediatric inflammatory bowel disease 105 samples shares patient-derived, organoids
- GSE287174 Patient-Derived Meningioma Organoids: A Reliable Model for Studying Human Tumor Pathophysiology 65 samples shares patient-derived, organoids
- GSE262110 Patient-derived response estimates from zero-passage organoids of luminal breast cancer 35 samples shares patient-derived, organoids
- GSE302327 HIF-1alpha activity affects stem cell fate in patient-derived ileum organoids 29 samples shares patient-derived, organoids
- GSE324866 1.Effects of L013 treatment on gene expression in KYSE150 and KYSE510 cells. 2. 5 Patient-derived organoids RNA-seq data 27 samples shares patient-derived, organoids
- GSE276387 Modeling Lung Adenocarcinoma Metastases Using Patient-Derived Organoids 26 samples shares patient-derived, organoids
- GSE267132 Drug Repurposing Using Molecular Network Analysis Identifies Janus Kinase as Targetable Driver in Necrobiosis Lipoidica 22 samples shares repurposing, drug
- GSE319077 Excitatory cortical neurons from CDKL5 deficiency disorder patient-derived organoids show early hyperexcitability not identified in neurogenin2 induced neurons [RNA-Seq] 18 samples shares patient-derived, organoids
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.