An axonal guidance cue Semaphorin 6D orchestrates systemic metabolism and myelopoiesis through tuning sympathetic innervation (epididymal white adipose tissue)
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × WT_CD vs 3 × WT_HFD vs 3 × KO_CD vs 3 × KO_HFDGroups 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
- Semaphorin 6D tunes amygdalar circuits for emotional, metabolic, and inflammatory outputsNeuron · 2024
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 GSE201216_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 PRJNA830436 and SRA study SRP371500. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM6052814 WT_CD_1 WT_CD
- GSM6052815 WT_CD_2 WT_CD
- GSM6052816 WT_CD_3 WT_CD
- GSM6052817 WT_HFD_1 WT_HFD
- GSM6052818 WT_HFD_2 WT_HFD
- GSM6052819 WT_HFD_3 WT_HFD
- GSM6052820 KO_CD_2 KO_CD
- GSM6052821 KO_CD_3 KO_CD
- GSM6052822 KO_CD_4 KO_CD
- GSM6052823 KO_HFD_1 KO_HFD
- GSM6052824 KO_HFD_4 KO_HFD
- GSM6052825 KO_HFD_5 KO_HFD
- GSE195825 An axonal guidance cue Semaphorin 6D orchestrates systemic metabolism and myelopoiesis through tuning sympathetic innervation 24 samples shares orchestrates, myelopoiesis, sympathetic, innervation, semaphorin, guidance, systemic
- GSE237201 ROCK1 orchestrates B cell differentiation in response to PAMPs and heme by controlling the heme-regulated proteins Bach2 and HRI 48 samples shares orchestrates
- GSE286424 A key role of PIEZO2 mechanosensitive ion channel in adipose sensory innervation [bulk RNA-seq] 46 samples shares innervation
- GSE255061 Phosphatase-independent activity of smooth-muscle calcineurin orchestrates a gene expression program leading to arterial hypertension 40 samples shares orchestrates
- GSE326648 Sexual dimorphism shapes AAK trajectory in Pax6 deficiency mouse model with early immune activation, impaired innervation, and altered tears 40 samples shares innervation
- GSE262587 TDG orchestrates ATF4-dependent gene transcription during retinoic acid-induced cell lineage committment 36 samples shares orchestrates
- GSE240912 Maternal IL-10 restricts fetal emergency myelopoiesis [Bulk RNA-seq] 36 samples shares myelopoiesis
- GSE269318 Cancer-intrinsic Cxcl5 orchestrates global metabolic reprogramming of three dimensional cancers by upregulating Hif1α and Myc expression 31 samples shares orchestrates
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.