Impaired oxysterol-liver X receptor signaling underlies aberrant cortical neurogenesis in a stem cell model of neurodevelopmental disorder
RNA-seq (gene expression) · human · 71 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
- 71 samples: 71 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.
- Paper
- Impaired oxysterol-liver X receptor signaling underlies aberrant cortical neurogenesis in a stem cell model of neurodevelopmental disorderCell 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 GSE119316_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 PRJNA488728 and SRA study SRP159245. 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 71 sample titles: 71 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.
- GSM3369827 CKO5A [neuroepithelium]
- GSM3369828 CKO5B [neuroepithelium]
- GSM3369829 CKO12A [neural progenitor cells]
- GSM3369830 CKO12B [neural progenitor cells]
- GSM3369831 CKO30A [neurons]
- GSM3369832 CKO30B [neurons]
- GSM3369833 CKO30C [neurons]
- GSM3369834 CAS905A [neuroepithelium]
- GSM3369835 CAS905B [neuroepithelium]
- GSM3369836 CAS905C [neuroepithelium]
- GSM3369837 CAS912A [neural progenitor cells]
- GSM3369838 CAS912B [neural progenitor cells]
- GSM3369839 CAS912C [neural progenitor cells]
- GSM3369840 CAS930A [neurons]
- GSM3369841 CAS930B [neurons]
- GSM3369842 CAS930C [neurons]
- GSM3369843 CKO05A [neuroepithelium]
- GSM3369844 H7d18A [neural progenitor cells]
- GSM3369845 H7d18B [neural progenitor cells]
- GSM3369846 H7d18C [neural progenitor cells]
- GSM3369847 COEd18B [neural progenitor cells]
- GSM3369848 COEd18C [neural progenitor cells]
- GSM3369849 H7d43A [neurons]
- GSM3369850 H7d43B [neurons]
- GSM3369851 H7d43C [neurons]
- GSM3369852 COEd43A [neurons]
- GSM3369853 COEd43B [neurons]
- GSM3369854 COEd43C [neurons]
- GSM3369855 H7d10A [neuroepithelium]
- GSM3369856 H7d10B [neuroepithelium]
- GSM3369857 H7d10C [neuroepithelium]
- GSM3369858 COEd10A [neuroepithelium]
- GSM3369859 COEd10B [neuroepithelium]
- GSM3369860 COEd10C [neuroepithelium]
- GSM3369861 COEd18A [neuroepithelium]
- GSM3369862 1 [neural progenitor cells]
- GSM3369863 2 [neural progenitor cells]
- GSM3369864 3 [neural progenitor cells]
- GSM3369865 4 [neural progenitor cells]
- GSM3369866 5 [neural progenitor cells]
+ 31 more — browse all 71 samples with per-sample file links →
- GSE325956 Thalamic NRXN1-Mediated Input to Human Cortical Progenitors Drives Excitatory Neurogenesis 43 samples shares neurogenesis, cortical
- GSE231321 Phosphorylation of 53BP1 by ATM enforce neurodevelopmental programs in cortical organoids 30 samples shares neurodevelopmental, cortical
- GSE299954 MeCP2 gene dosage-dependent neurodevelopmentally restricted defects arise by SWI/SNF-mediated aberrant activation of cell fate-determining bivalent genes [RNA-Seq] 18 samples shares neurodevelopmental, aberrant
- GSE266030 The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome [RNA-seq] 9 samples shares neurogenesis, cortical
- GSE275931 Exposure to the antiretroviral drug dolutegravir impairs structure and neurogenesis in a forebrain organoid model of human embryonic cortical development 6 samples shares neurogenesis, cortical
- GSE249942 Requirements for the neurodevelopmental disorder-associated gene ZNF292 in human cortical interneuron development and function 55 samples shares neurodevelopmental, cortical
- GSE266032 The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome. 29 samples shares neurogenesis, cortical
- GSE266029 The chromatin remodeler CHD1L controls human cortical neurogenesis and contributes to distal 1q21.1 deletion/duplication syndrome [ATAC-seq] 12 samples shares neurogenesis, cortical
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.