Mouse PVN CRH neurons — early-life adversity (scRNA-seq)
Mus musculus · Paraventricular nucleus · scRNA-seq
Selected data and study scope
This dataset contains scRNA-seq data from Mus musculus, sampled from paraventricular nucleus. The default comparison examines gene expression in Early-life adversity relative to Control rearing.
The explorer includes 1 track and 1 comparison for this dataset.
The default track, PVN CRH neurons (animal pseudobulk), includes 14 Control rearing samples and 10 Early-life adversity samples in this comparison. These are analysis sample counts. Check the source for biological replication and pooling.
Interpretation and limitations
The source assay profiles individual cells. The track and sample counts shown here describe the analysis used for the comparison. Cell counts do not replace independent biological replicates.
Expression values are CPM (TMM-normalized): counts per million on library sizes adjusted by the TMM factors of the study’s own edgeR fit. This scale adjusts for library size and composition, not gene length. Use it to inspect a feature across the samples in this analysis. CPM values are not absolute transcript counts.
Evidence and verification
Pipeline QC passed. Mouse PVN CRH neurons — early-life adversity (scRNA-seq); all 1 registered contrasts on default track crh_pvn
Experimental design passed. Mouse PVN CRH neurons — early-life adversity (scRNA-seq); all 1 registered contrasts on default track crh_pvn
Author concordance not assessed. Author effect concordance has not been assessed
Pipeline QC can pass while experimental-design limitations remain. Read both assessments before interpreting results.
Open the dataset in the Explorer to read each check and its evidence. Author concordance compares effects for matched genes. It does not require identical author P values or FDR.
Read the analysis methods and interpretation guide and how to cite the source study and HypoExplorer. The source publication may include tissues, groups or comparisons beyond the data shown here.
Source study
PVN CRH-expressing cells collected at P10-P12 after limited-bedding early-life adversity; 602 deposited cells were aggregated to 24 litter pseudobulks: 14 control litters containing 50 pups and 10 ELA litters containing 38 pups. Age at collection is modeled. Batch-L13 follows the author supplement LBN assignment despite deposited CTL labels; the author post-QC set of 511 cells is not reproduced (Short et al., Biol Psychiatry Glob Open Sci 2021, PMID 36712559; GSE174085)
Source publication
Short AK, Thai CW, Chen Y, Kamei N, Pham AL, Birnie MT, et al.
Biological psychiatry global open science · 2023
Repository study title
Single-Cell Transcriptomics of hypothalamic CRH-expressing neurons informs mechanisms by which Early-Life Adversity sculpts stress-responses enduringly
The original study authors produced these data. HypoExplorer displays selected data and analyses that may cover only part of the study.
Comparisons in HypoExplorer
Early-life adversity vs Control rearing · default
Positive differential-expression values indicate higher expression in the case group relative to the baseline. Check the comparison direction and study design when interpreting results.
Available tracks
| Track | Features | Control rearing n | Early-life adversity n |
|---|---|---|---|
| PVN CRH neurons (animal pseudobulk) | 24,181 | 14 | 10 |
Expression and analysis results
Open this dataset to inspect gene expression and differential-expression results across the available tracks. Pathway enrichment is also available. The pathway databases differ by dataset.
HypoExplorer is in beta testing. Features and analyses may change during testing. Review the original source, analysis methods and quality-control checks before using a result in research.