Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor [RNA-seq]
RNA-seq (gene expression) · human · 36 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
- 36 samples: 28 distinct titles, 6 of them repeatedGroups 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
- ZIC1 is a context-dependent medulloblastoma driver in the rhombic lipNature genetics · 2025
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 GSE217571_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 PRJNA899858 and SRA study SRP407040. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 36 sample titles: 28 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.
- GSM6721862 ATOH1_GFP_RNA_mch_bulk_rep1
- GSM6721863 ATOH1_GFP_RNA_mch_bulk_rep2
- GSM6721864 ATOH1_GFP_RNA_mch_sort_rep1
- GSM6721865 ATOH1_GFP_RNA_mch_sort_rep2
- GSM6721866 ATOH1_GFP_RNA_ZIC1_bulk_rep1
- GSM6721867 ATOH1_GFP_RNA_ZIC1_bulk_rep2
- GSM6721868 ATOH1_GFP_RNA_ZIC1_sort_rep1
- GSM6721869 ATOH1_GFP_RNA_ZIC1_sort_rep2
- GSM6721871 D283_ev1_ZIC1_mut_constructs_RNA
- GSM6721872 D283_ev2_ZIC1_mut_constructs_RNA
- GSM6721873 D283_P301S_ZIC1_mut_constructs_RNA
- GSM6721874 D283_R294C_ZIC1_mut_constructs_RNA
- GSM6721875 D283_S399F_ZIC1_mut_constructs_RNA
- GSM6721876 D283_S403F_ZIC1_mut_constructs_RNA
- GSM6721877 D283_WT1_ZIC1_mut_constructs_RNA
- GSM6721878 D283_WT2_ZIC1_mut_constructs_RNA
- GSM6721879 D425_ev1_ZIC1_mut_constructs_RNA
- GSM6721880 D425_ev2_ZIC1_mut_constructs_RNA
- GSM6721881 D425_P301S_ZIC1_mut_constructs_RNA
- GSM6721882 D425_R294C_ZIC1_mut_constructs_RNA
- GSM6721883 D425_RNA_BFP1
- GSM6721884 D425_RNA_BFP2
- GSM6721885 D425_RNA_BFP3
- GSM6721886 D425_RNA_ZIC1_4_1
- GSM6721887 D425_RNA_ZIC1_4_2
- GSM6721888 D425_RNA_ZIC1_4_3
- GSM6721889 D425_S399F_ZIC1_mut_constructs_RNA
- GSM6721890 D425_S403F_ZIC1_mut_constructs_RNA
- GSM6721891 D425_WT1_ZIC1_mut_constructs_RNA
- GSM6721892 D425_WT2_ZIC1_mut_constructs_RNA
- GSM8501021 MB051_BFP_1_RNA
- GSM8501022 MB051_BFP_2_RNA
- GSM8501023 MB051_BFP_3_RNA
- GSM8501024 MB051_ZIC_1/4_1_RNA
- GSM8501025 MB051_ZIC_1/4_2_RNA
- GSM8501026 MB051_ZIC_1/4_3_RNA
- GSE217639 Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor 49 samples shares zic1, medulloblastoma, progenitor, granule, neuron, group, lines
- GSE232586 Compared with the Mock group, FGF8+10 treatment mature the differentiated LPM-like cells to form LM-like cells, and gene expression profile at single cell level of Msx1+ mesenchymal progenitors from mouse E10.5 embryos 9 samples shares progenitor, group
- GSE301654 scRNA-seq of primary mouse and human cerebellar nestin-expressing progenitor neurosphere cultures 1 samples shares progenitor, rna-seq
- GSE294901 Measles oncolytic virus as an immunotherapy for recurrent/refractory pediatric medulloblastoma and atypical teratoid rhabdoid tumor: results from PNOC005 84 samples shares medulloblastoma
- GSE204785 Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress 39 samples shares granule
- GSE312133 Intrinsic mechanisms and microenvironmental cues fine-tune plasticity of esophageal progenitors 26 samples shares progenitor
- GSE294342 ALDH1A1+ cells are endometrial progenitors contributing to regeneration and endometriosis 20 samples shares progenitor
- GSE326194 Distinct signalling centre and progenitor identity dynamics initiate human forebrain patterning 16 samples shares progenitor
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.