Generation of human cerebral organoids with a structured outer subventricular zone
RNA-seq (gene expression) · human · 15 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
- 15 samples: 6 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
- Generation of human cerebral organoids with a structured outer subventricular zoneCell reports · 2024
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 GSE224346_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 PRJNA930689 and SRA study SRP420643. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 15 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.
- GSM7020130 H9_Control1_d40 H9_Control1_d
- GSM7020131 H9_Control2_d40 H9_Control2_d
- GSM7020132 H9_LIF1_d40 H9_LIF1_d
- GSM7020133 H9_LIF2_d40 H9_LIF2_d
- GSM7020134 H9_Control1_d60 H9_Control1_d
- GSM7020135 H9_Control2_d60 H9_Control2_d
- GSM7020136 H9_LIF1_d60 H9_LIF1_d
- GSM7020137 H9_LIF2_d60 H9_LIF2_d
- GSM7020138 H9_H9_d100_Control1 H9_H9_d100_Control
- GSM7020139 H9_H9_d100_Control2 H9_H9_d100_Control
- GSM7020140 H9_H9_d100_LIF1 H9_H9_d100_LIF
- GSM7020141 H9_H9_d100_LIF2 H9_H9_d100_LIF
- GSM7020142 H9_Control_a_d65
- GSM7020143 H9_LIF_a_d65
- GSM7020144 H9_pericyte_a_d65
- GSE292624 Dissociated human cerebral organoids on micro-electrode arrays develop neuronal networks 13 samples shares organoids, cerebral
- GSE263425 Modeling the Blood-Brain Barrier Formation and Cerebral Cavernous Malformations in human PSCs- and primary tissue-derived organoids 12 samples shares organoids, cerebral
- GSE319124 Next-GenerationPediatric Cancer Models: Patient-Matched Orthotopic Xenografts, 3D Organoids, 2D Cultures, and Cell Lines for Identification of Therapeutic Vulnerabilities in Pediatric Solid Tumors [scRNAseq] 59 samples shares generation, organoids
- GSE298576 Mass generation and long-term expansion of hepatocyte organoids from adult primary hepatocytes 24 samples shares generation, organoids
- GSE327431 Halofantrine protects photoreceptors in multiple models of retinal degeneration [organoids] 15 samples shares generation, organoids
- GSE281002 Rapid generation of functional vascular organoids via simultaneous transcription factor activation of endothelial and mural lineages 15 samples shares generation, organoids
- GSE277967 Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols [time-course bulk RNA-seq] 768 samples shares organoids
- GSE272333 TOWARDS THE GENERATION OF A LASER CAPTURE MICRODISSECTION-BASED HUMAN ANAGEN HAIR FOLLICLE TRANSCRIPTOME ATLAS 110 samples shares generation
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.