Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytes [bulk RNA-seq]
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 18 samples: 12 distinct titles, 2 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
- Autism-associated CHD8 controls reactive gliosis and neuroinflammation via remodeling chromatin in astrocytesCell reports · 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 GSE271650_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 PRJNA1132694 and SRA study SRP518352. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 18 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.
- GSM8381189 Cortex, Saline, 3days, Control Saline Sample 1
- GSM8381190 Cortex, Saline, 3days, Control Saline Sample 3
- GSM8381191 Cortex, Saline, 3days, Control Saline Sample 5
- GSM8381192 Cortex, Saline, 3days, Control Saline Sample 7
- GSM8381193 Cortex, Saline, 3days, cKO Saline Sample 2
- GSM8381194 Cortex, Saline, 3days, cKO Saline Sample 4
- GSM8381195 Cortex, Saline, 3days, cKO Saline Sample 6
- GSM8381196 Cortex, Saline, 3days, cKO Saline Sample 8
- GSM8381197 Cortex, Saline, 3days, Control LPS Sample A1
- GSM8381198 Cortex, Saline, 3days, Control LPS Sample B2
- GSM8381199 Cortex, Saline, 3days, Control LPS Sample C3
- GSM8381200 Cortex, Saline, 3days, Control LPS Sample K11
- GSM8381201 Cortex, Saline, 3days, Control LPS Sample L12
- GSM8381202 Cortex, Saline, 3days, cKO LPS Sample D4
- GSM8381203 Cortex, Saline, 3days, cKO LPS Sample E5
- GSM8381204 Cortex, Saline, 3days, cKO LPS Sample F6
- GSM8381205 Cortex, Saline, 3days, cKO LPS Sample M13
- GSM8381206 Cortex, Saline, 3days, cKO LPS Sample N14
- GSE279810 Genetic and epigenetic regulation of Treg cell fitness by autism-related chromatin remodeler CHD8 18 samples shares chd8, chromatin
- GSE274492 The remodeling of bivalent chromatin is essential for mouse peri-implantation embryogenesis [Valid RNA-Seq] 200 samples shares remodeling, chromatin
- GSE300757 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages 127 samples shares remodeling, chromatin
- GSE299114 Endothelial Cells retain inflammatory memory through chromatin remodeling [RNA-Seq 2] 53 samples shares remodeling, chromatin
- GSE290680 Nuclear class 3 PI3K co-activates fasting-specific chromatin remodeling 36 samples shares remodeling, chromatin
- GSE239469 Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling [RNA-seq] 28 samples shares remodeling, chromatin
- GSE327619 Murine Endothelial Chromatin Remodeling Enzymes Modulate Plasmin Activity and Sterile Inflammation to Prevent Lethal Embryonic Liver Deterioration 24 samples shares remodeling, chromatin
- GSE267688 Autism-associated mutations in Kdm6b affect its role as a chromatin regulator in brain development 20 samples shares autism-associated, chromatin
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.