SHANK3 deficiency alters early progenitor dynamics and reveals shared pathways with neurodegeneration
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.
- Paper
- "SHANK3 deficiency alters early progenitor dynamics and reveals shared pathways with neurodegeneration"Molecular psychiatry · 2026
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 GSE281741_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 PRJNA1185628 and SRA study SRP545105. 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.
- GSM8627404 P1-cl1, SHANK3 deletion
- GSM8627405 P2-cl5, SHANK3 deletion
- GSM8627406 P2.2-cl6, SHANK3 deletion
- GSM8627407 P4-cl1, SHANK3 deletion
- GSM8627408 P5-cl1, SHANK3 deletion
- GSM8627409 P6-cl2, SHANK3 deletion
- GSM8627410 P9-cl1, SHANK3 deletion
- GSM8627411 P11-cl1, SHANK3 point mutation
- GSM8627412 P12-cl1, SHANK3 point mutation
- GSM8627413 P14-cl1, SHANK3 point mutation
- GSM8627414 C1-cl1, control
- GSM8627415 C2-cl1, control
- GSM8627416 C3-cl1, control
- GSM8627417 C4-cl1, control
- GSM8627418 C5-cl1, control
- GSM8627419 C6-cl3, control
- GSM8627420 C7-cl3, control
- GSM8627421 Ed1-cl1, isogenic, SHANK3 point mutation
- GSE296649 Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML [scRNA-Seq] 58 samples shares progenitor, early
- GSE284387 DNMT1 RFTS mutation alters RNA splicing and drives neurodegeneration via its RNA-binding function [RNA-Seq] 26 samples shares neurodegeneration, alters
- GSE296381 Clonal evolution permits outgrowth of chemoresistant LMPP-like early progenitors in relapsed NPM1c AML 20 samples shares progenitor, early
- GSE284549 RFTS mutation alters RNA splicing and drives neurodegeneration via its RNA-binding function 47 samples shares neurodegeneration, alters
- GSE271127 Substained DNA demethylation and discordant chromatin accessibility dynamics define enhancer regulation during neural progenitor cell differentiation [ATACme] 18 samples shares progenitor, dynamics
- GSE302350 KMT2D-deficiency destabilizes lineage progression in immature neural progenitors 16 samples shares deficiency, progenitor
- GSE301514 ID3 Deficiency Alters Chromatin Accessibility at DSB Sites and Enhances Vulnerability to HDAC Inhibition [ATAC-seq] 12 samples shares deficiency, alters
- GSE280113 Progenitor effects and unique transcriptomic signatures linked to differentiation phenotype in clonally expanded antigen-specific CD8 T memory stem cells (TSCM) 509 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.