Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [scRNA-seq]
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.
- Organism
- Homo sapiens (human)
- Samples
- 12 samples: 12 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
- Longitudinal multi-omics reveals pathogenic TSC2 variants disrupt developmental trajectories of human cortical organoids derived from Tuberous Sclerosis ComplexbioRxiv : the preprint server for biology · 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 GSE247368_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 PRJNA1037170 and SRA study SRP470972. 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 12 sample titles: 12 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.
- GSM7887924 SingleCell_CTRL_C1-A
- GSM7887925 SingleCell_CTRL_C1-B
- GSM7887926 SingleCell_CTRL_C2-A
- GSM7887927 SingleCell_CTRL_C2-B
- GSM7887928 SingleCell_CTRL_C3-A
- GSM7887929 SingleCell_CTRL_C3-B
- GSM7887930 SingleCell_TSC_T1-A
- GSM7887931 SingleCell_TSC_T1-B
- GSM7887932 SingleCell_TSC_T2-A
- GSM7887933 SingleCell_TSC_T2-B
- GSM7887934 SingleCell_TSC_T3-A
- GSM7887935 SingleCell_TSC_T3-B
- GSE247369 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks 92 samples shares tsc2, communication, trajectories, pathogenic, organoids, cell-cell, variants
- GSE247367 Pathogenic TSC2 variants alter developmental trajectories of human cortical organoids and perturb cell-cell communication networks [bulk RNA-seq] 80 samples shares tsc2, communication, trajectories, pathogenic, organoids, cell-cell, variants
- GSE296243 Genomic and Immune Landscape of Pancreatic Ductal Adenocarcinoma Associated with Germline Pathogenic Variants in ATM 24 samples shares pathogenic, variants
- GSE242346 Human stem cells with in vivo high plasticity generated by cell-cell communication 22 samples shares communication, cell-cell
- GSE301142 Multiple mechanisms lead to differential loss-of-function effects of pathogenic SARS2 variants: implications for genotype-phenotype analyses 18 samples shares pathogenic, variants
- GSE266958 Pathogenic PPP2R5D variants alters the transcriptome of patient iPSC-derived glutamatergic neurons 18 samples shares pathogenic, variants
- GSE292979 Characterisation of a pathogenic non-migratory fibroblast population in systemic sclerosis skin [scRNA-Seq] 15 samples shares pathogenic, scrna-seq
- GSE288121 Pathogenic variants in the splicing factor SF1 lead to a new neurodevelopmental disorder. 12 samples shares pathogenic, variants
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.