JAX Study 11- RNA-seq of male KOLF2.2J hiPSC-derived cortical brain organoids during different time points.
RNA-seq (gene expression) · human · 18 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
- 18 samples: 18 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 GSE303979_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 PRJEB91184 and SRA study ERP174176. 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 18 sample titles: 18 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.
- GSM9140091 CBO-KOLF2.2J_Day3-WT1, WT
- GSM9140092 CBO-KOLF2.2J_Day3-WT2, WT
- GSM9140093 CBO-KOLF2.2J_Day3-WT4, WT
- GSM9140094 CBO-KOLF2.2J_Day4-WT2, WT
- GSM9140095 CBO-KOLF2.2J_Day4-WT3, WT
- GSM9140096 CBO-KOLF2.2J_Day4-WT4, WT
- GSM9140097 CBO-KOLF2.2J_Day5-WT1, WT
- GSM9140098 CBO-KOLF2.2J_Day5-WT2, WT
- GSM9140099 CBO-KOLF2.2J_Day5-WT4, WT
- GSM9140100 CBO-KOLF2.2J_Day20-WT1, WT
- GSM9140101 CBO-KOLF2.2J_Day20-WT3, WT
- GSM9140102 CBO-KOLF2.2J_Day20-WT4, WT
- GSM9140103 CBO-KOLF2.2J_Day25-WT1, WT
- GSM9140104 CBO-KOLF2.2J_Day25-WT2, WT
- GSM9140105 CBO-KOLF2.2J_Day25-WT4, WT
- GSM9140106 CBO-KOLF2.2J_Day32-WT1, WT
- GSM9140107 CBO-KOLF2.2J_Day32-WT2, WT
- GSM9140108 CBO-KOLF2.2J_Day32-WT3, WT
- GSE287843 JAX Study 4- RNA-seq of male KOLF2.2J hiPSC-derived cortical brain organoids and extra-embryonic lineages homozygous null for six different transcription factors 28 samples shares kolf2, jax, hipsc-derived, organoids, different, cortical, rna-seq
- GSE318601 Early differential impact of MeCP2 mutations on functional networks in Rett syndrome patient-derived human cortical organoids [RNA-Seq] 8 samples shares organoids, different, cortical, rna-seq
- GSE247368 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [scRNA-seq] 12 samples shares organoids, cortical, rna-seq
- GSE299831 KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [RNA-seq] 12 samples shares kolf2, rna-seq
- GSE277967 Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols [time-course bulk RNA-seq] 768 samples shares organoids, rna-seq
- GSE334500 Psychotropic-drug and neurotransmitter perturbation RNA-seq of human iPSC-derived cardiac and retinal organoids (ToxiPred) 96 samples shares organoids, rna-seq
- GSE228249 Transcriptome analysis of primary human hepatocytes-derived organoids [RNA-seq] 82 samples shares organoids, rna-seq
- GSE279590 BMP, MEK and WNT modulation with NGN2 expression for rapid generation of hiPSC-derived neurons amenable to regional patterning [bulk RNA-seq] 61 samples shares hipsc-derived, rna-seq
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.