Generation of human induced pluripotent stem cell-derived 3D human cortical, striatal, mesencephalic and diencephalic organoids
Single-cell RNA-seq · human · 12 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Homo sapiens (human)
- Samples
- 12 samples: 2 × D100_1205-4_hStrO vs 2 × D100_1205-4_hMeO vs 2 × D100_1205-4_hDiOGroups 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 GSE279264_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA1171745. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 6 samples.
How we read this: 3 replicated groups read from 12 sample titles; they account for 6 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.
- GSM8565535 D113_1208-2_hCO_1
- GSM8565536 D100_1205-4_hCO_2
- GSM8565537 D128_1205-4_hCO_3
- GSM8565538 D100_1205-4_hStrO_4 D100_1205-4_hStrO
- GSM8565539 D100_1208-2_hStrO_5
- GSM8565540 D100_1205-4_hStrO_6 D100_1205-4_hStrO
- GSM8565541 D100_1205-4_hMeO_7 D100_1205-4_hMeO
- GSM8565542 D100_1208-2_hMeO_8
- GSM8565543 D100_1205-4_hMeO_9 D100_1205-4_hMeO
- GSM8565544 D100_1205-4_hDiO_10 D100_1205-4_hDiO
- GSM8565545 D100_1208-2_hDiO_11
- GSM8565546 D100_1205-4_hDiO_12 D100_1205-4_hDiO
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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.