Disruption of the intellectual disability-linked gene Hs6st2 in mice decreases heparan sulfate 6-O-sulfation in the brain and impairs memory
RNA-seq (gene expression) · mouse · 15 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
- Mus musculus (mouse)
- Samples
- 15 samples: 4 × hippocampus_WT vs 4 × hippocampus_KO vs 4 × cortex_WT vs 3 × cortex_KOGroups 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
- Knockout of the intellectual disability-linked gene Hs6st2 in mice decreases heparan sulfate 6-O-sulfation, impairs dendritic spines of hippocampal neurons, and affects memoryGlycobiology · 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 GSE213745_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 PRJNA882373 and SRA study SRP398203. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 4 replicated groups read from 15 sample titles; they account for 15 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.
- GSM6593358 hippocampus_WT_Rep1 hippocampus_WT
- GSM6593359 hippocampus_WT_Rep2 hippocampus_WT
- GSM6593360 hippocampus_WT_Rep3 hippocampus_WT
- GSM6593361 hippocampus_WT_Rep4 hippocampus_WT
- GSM6593362 hippocampus_KO_Rep1 hippocampus_KO
- GSM6593363 hippocampus_KO_Rep2 hippocampus_KO
- GSM6593364 hippocampus_KO_Rep3 hippocampus_KO
- GSM6593365 hippocampus_KO_Rep4 hippocampus_KO
- GSM6593366 cortex_WT_Rep1 cortex_WT
- GSM6593367 cortex_WT_Rep2 cortex_WT
- GSM6593368 cortex_WT_Rep3 cortex_WT
- GSM6593369 cortex_WT_Rep4 cortex_WT
- GSM6593370 cortex_KO_Rep1 cortex_KO
- GSM6593371 cortex_KO_Rep2 cortex_KO
- GSM6593372 cortex_KO_Rep3 cortex_KO
- GSE240887 The intellectual disability risk gene Kdm5b regulates long term memory consolidation in the hippocampus 44 samples shares intellectual
- GSE252400 Epigenetic Modulation to perturb the SYNGAP1 Intellectual Disability (ID) that ameliorates synaptic and behavioural deficits 18 samples shares intellectual
- GSE313803 HNRNPH2 variant linked to intellectual disability disrupts myelination by impairing oligodendrocyte differentiation 7 samples shares intellectual
- GSE44746 Loss of cytosine-5 methylation in tRNA triggers stress responses in a disease model for Intellectual Disability 21 samples shares intellectual
- GSE290539 Chronic administration of a HDAC inhibitor boosts microglial differentiation and treats neurological disease in a mouse model of intellectual disability. 16 samples shares intellectual
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.