Cognitive and Synaptic Impairment Induced by Deficiency of Autism Risk Gene Smarcc2 and its Rescue by Histone Deacetylase Inhibition
RNA-seq (gene expression) · human · 16 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
- 16 samples: 4 × GFP vs 4 × SMARCC2kd vs 4 × hipsc_ASD vs 4 × hipsc_young_controlGroups 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.
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 GSE327210_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 PRJNA1449491 and SRA study SRP689628. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 of them. 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.
- GSM9651287 GFP_1 GFP
- GSM9651288 GFP_2 GFP
- GSM9651289 GFP_3 GFP
- GSM9651290 GFP_4 GFP
- GSM9651291 SMARCC2kd_1 SMARCC2kd
- GSM9651292 SMARCC2kd_2 SMARCC2kd
- GSM9651293 SMARCC2kd_3 SMARCC2kd
- GSM9651294 SMARCC2kd_4 SMARCC2kd
- GSM9651295 hipsc_ASD_1 hipsc_ASD
- GSM9651296 hipsc_ASD_2 hipsc_ASD
- GSM9651297 hipsc_ASD_3 hipsc_ASD
- GSM9651298 hipsc_ASD_4 hipsc_ASD
- GSM9651299 hipsc_young_control_1 hipsc_young_control
- GSM9651300 hipsc_young_control_2 hipsc_young_control
- GSM9651301 hipsc_young_control_3 hipsc_young_control
- GSM9651302 hipsc_young_control_4 hipsc_young_control
- GSE243750 SEX-DEPENDENT APOE4 NEUTROPHIL-MICROGLIA INTERACTIONS DRIVE COGNITIVE IMPAIRMENT IN ALZHEIMER'S DISEASE 288 samples shares impairment, cognitive
- GSE263125 Macrophage-induced enteric neurodegeneration leads to motility impairment during gut inflammation 23 samples shares impairment, induced
- GSE266298 Epigenetic changes by EZH2 inhibition increase translocations in B cells with high AID activity or DNA repair deficiency 130 samples shares deficiency, inhibition
- GSE267775 KMT2C Deficiency Drives Luminal Transdifferentiation into Double-Negative Prostate Cancer and Sensitizes to Fatty Acid Synthase Inhibition [CUT&Tag] 26 samples shares deficiency, inhibition
- GSE297959 De novo mutations in the MiDAC HDAC complex cause a neurodevelopmental 2 syndrome resulting from increased deacetylase activity [RNA-seq] 18 samples shares deacetylase
- GSE245463 Prediction and validation of a human immunodeficiency with CRISPR 14 samples shares deficiency
- GSE241047 PRDM16 deficiency triggered by TGF-β1 signaling promotes aberrant mitochondrial homeostasis and kidney fibrosis 11 samples shares deficiency
- GSE319635 Methionine and choline deficiency rewires transcriptional programs to recapitulate molecular features of human MASH 8 samples shares deficiency
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.