APOE4 impacts cortical neurodevelopment and alters network formation in human brain organoids
RNA-seq (gene expression) · human · 32 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
- 32 samples: 16 conditions, mostly in duplicateGroups 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
- APOE4 impacts cortical neurodevelopment and alters network formation in human brain organoidsStem cell reports · 2025
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 GSE289912_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 PRJNA1225283 and SRA study SRP564773. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 32 samples.
How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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.
- GSM8801362 120DIV_37A3_CO1 120DIV_37A3_CO
- GSM8801363 120DIV_37A3_CO2 120DIV_37A3_CO
- GSM8801364 30DIV_37A3_CO1 30DIV_37A3_CO
- GSM8801365 30DIV_37A3_CO2 30DIV_37A3_CO
- GSM8801366 120DIV_37A3_GEO1 120DIV_37A3_GEO
- GSM8801367 120DIV_37A3_GEO2 120DIV_37A3_GEO
- GSM8801368 30DIV_37A3_GEO1 30DIV_37A3_GEO
- GSM8801369 30DIV_37A3_GEO2 30DIV_37A3_GEO
- GSM8801370 120DIV_37A4_CO1 120DIV_37A4_CO
- GSM8801371 120DIV_37A4_CO2 120DIV_37A4_CO
- GSM8801372 30DIV_37A4_CO1 30DIV_37A4_CO
- GSM8801373 30DIV_37A4_CO2 30DIV_37A4_CO
- GSM8801374 120DIV_37A4_GEO1 120DIV_37A4_GEO
- GSM8801375 120DIV_37A4_GEO2 120DIV_37A4_GEO
- GSM8801376 30DIV_37A4_GEO1 30DIV_37A4_GEO
- GSM8801377 30DIV_37A4_GEO2 30DIV_37A4_GEO
- GSM8801378 30DIV_11A4_CO1 30DIV_11A4_CO
- GSM8801379 30DIV_11A4_CO2 30DIV_11A4_CO
- GSM8801380 120DIV_11A4_CO1 120DIV_11A4_CO
- GSM8801381 120DIV_11A4_CO2 120DIV_11A4_CO
- GSM8801382 30DIV_11A4_GEO1 30DIV_11A4_GEO
- GSM8801383 30DIV_11A4_GEO2 30DIV_11A4_GEO
- GSM8801384 120DIV_11A4_GEO1 120DIV_11A4_GEO
- GSM8801385 120DIV_11A4_GEO2 120DIV_11A4_GEO
- GSM8801386 30DIV_11A3_CO1 30DIV_11A3_CO
- GSM8801387 30DIV_11A3_CO2 30DIV_11A3_CO
- GSM8801388 120DIV_11A3_CO1 120DIV_11A3_CO
- GSM8801389 120DIV_11A3_CO2 120DIV_11A3_CO
- GSM8801390 30DIV_11A3_GEO1 30DIV_11A3_GEO
- GSM8801391 30DIV_11A3_GEO2 30DIV_11A3_GEO
- GSM8801392 120DIV_11A3_GEO1 120DIV_11A3_GEO
- GSM8801393 120DIV_11A3_GEO2 120DIV_11A3_GEO
- GSE247368 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [scRNA-seq] 12 samples shares organoids, cortical, network
- GSE318601 Early differential impact of MeCP2 mutations on functional networks in Rett syndrome patient-derived human cortical organoids [RNA-Seq] 8 samples shares organoids, cortical, network
- GSE304228 Elucidating the role of DEAF1 in neurodevelopment and shared molecular pathways in high-risk autism genes using cortical organoids 11 samples shares neurodevelopment, organoids, cortical
- GSE267990 Mutant GFAP alters lineage commitment of neural organoids [AxDorganoids_bulk_experiment2] 47 samples shares organoids, alters
- GSE292624 Dissociated human cerebral organoids on micro-electrode arrays develop neuronal networks 13 samples shares organoids, network
- GSE286874 Triglyceride metabolism controls inflammation and microglial phenotypes associated with APOE4 [RNA-seq] 26 samples shares apoe4
- GSE254205 APOE4/4 is linked to damaging lipid droplets in Alzheimer's microglia 102 samples shares apoe4
- GSE277967 Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols [time-course bulk RNA-seq] 768 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.