m6Am-seq profiling of macrophage-specific Pcif1 knockout mice during experimental colitis
RNA-seq (gene expression) · mouse · 8 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
- 8 samples: 2 × FTO vs 2 × m7G_IP vs 2 × non_FTO vs 2 × InputGroups 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 GSE334689_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 PRJNA1476171 and SRA study SRP707730. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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.
- GSM9793358 FTO_1 FTO
- GSM9793359 FTO_2 FTO
- GSM9793360 m7G_IP_1 m7G_IP
- GSM9793361 m7G_IP_2 m7G_IP
- GSM9793362 non_FTO_1 non_FTO
- GSM9793363 non_FTO_2 non_FTO
- GSM9793364 Input_1 Input
- GSM9793365 Input_2 Input
- GSE280875 Transcriptomics profiling of gonadal white adipose tissue (gWAT) of wild-type (WT) and macrophage-specific Bnip3 knockout (MKO) mice fed a normal chow diet (NCD) or high-fat diet (HFD) 12 samples shares macrophage-specific, knockout
- GSE190710 Identifying Macrophage-specific L13a Knockout Transcriptomic Signatures 18 samples shares macrophage-specific, knockout
- GSE223224 Thymopentin ameliorates experimental colitis by inhibiting neutrophil extracellular traps: an alternative way to restore immune balance in IBD? 12 samples shares experimental, colitis
- GSE243307 A hepatocyte-specific transcriptional program driven by Rela and Stat3 exacerbates experimental colitis in mice by modulating bile synthesis 12 samples shares experimental, colitis
- GSE328526 Eosinophil-derived COX-2 protects against experimental colitis through the PGE2–IL-22 axis 4 samples shares experimental, colitis
- GSE287323 Transcriptomic profiling of oligodendrocytes, astrocytes, and microglia in an experimental autoimmune encephalomyelitis (EAE) model of demyelination 19 samples shares experimental
- GSE253318 Transcriptional profiling and multiple machine learning methods identified novel microglia biomarkers for Experimental Autoimmune Encephalomyelitis 16 samples shares experimental
- GSE326335 Bulk RNA Sequencing of Chimera-Derived Monocyte-Derived Macrophages Targeted for Mitochondrial ROS During Peak Experimental Autoimmune Encephalomyelitis 14 samples shares experimental
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.