Hypoxic injury triggers maladaptive repair in human kidney organoids
RNA-seq (gene expression) · human · 16 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
- 16 samples: 16 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE242426_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 PRJNA1013401 and SRA study SRP447128. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 16 sample titles: 16 distinct titles with little repetition. 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.
- GSM7528889 d20_Norm1_S1
- GSM7528890 d20_Norm2_S2
- GSM7528891 d20_Norm3_S3
- GSM7528892 d20_Hyp1_S4
- GSM7528893 d20_Hyp2_S5
- GSM7528894 d20_Hyp3_S6
- GSM7528895 d25_Norm1_S7
- GSM7528896 d25_Norm2_S8
- GSM7528897 d25_Norm3_S9
- GSM7528898 d25_Hyp1_S10
- GSM7528899 d25_Hyp2_S11
- GSM7528900 d25_Hyp3_S12
- GSM7763428 D20organoids-FB
- GSM7763429 D20organoids-GEX
- GSM7763430 D25organoids-FB
- GSM7763431 D25organoids-GEX
- GSE236379 Hypoxia Triggers Signatures of Maladaptive Repair in Human Kidney Organoids [bulk RNA-seq] 12 samples shares maladaptive, organoids, triggers, repair, kidney
- GSE259376 Establishment of epithelial inflammatory injury model using adult kidney organoids [RNA-seq] 16 samples shares organoids, injury, kidney
- GSE299171 Hypoimmunogenic hPSC-derived cardiac organoids for immune evasion and heart repair [bulkRNA-seq] 48 samples shares organoids, repair
- GSE249492 ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response 280 samples shares triggers, repair
- GSE277922 Chromatin Accessibility Analysis Reveals Regulatory Dynamics in hESC-Derived Kidney Organoids 25 samples shares organoids, kidney
- GSE277967 Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols [time-course bulk RNA-seq] 768 samples shares organoids
- GSE210993 RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids 103 samples shares organoids
- GSE334500 Psychotropic-drug and neurotransmitter perturbation RNA-seq of human iPSC-derived cardiac and retinal organoids (ToxiPred) 96 samples shares 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.