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BAI1 localises AMPA receptors at the cochlear afferent postsynaptic density and is

GSE254269 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2024/03/27 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 20 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: 20 samples: 7 × Bai1KO_P7_Het vs 7 × Bai1KO_P7_Homo vs 3 × Bai1KO_P22_Het vs 3 × Bai1KO_P22_HomoGroups 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: BAI1 localizes AMPA receptors at the cochlear afferent post-synaptic density and is essential for hearingCell reports · 2024

Summary (written by the submitters)

Type I spiral ganglion neurons (SGNs) convey sound information to the central auditory pathway by forming axo-somatic synapses with inner hair cells (IHCs), the primary sensory receptors of the mammalian cochlea. Although IHC ribbon synapses have been extensively studied, the molecular mechanisms regulating the structure and function of the post-synaptic density (PSD) at the SGN afferent terminals are largely unknown.

Read the full summary ↓

Using functional, morphological, and transcriptomic approaches, we demonstrate that brain-specific angiogenesis inhibitor 1 (BAI1), encoded by the Adgrb1 gene, is required for the clustering of the glutamate AMPA receptors GluR2-4 to the SGN post-synaptic density. Adult mice expressing BAI1 lacking the N-terminal thrombospondin type 1 repeats (TRS) have functional IHC synapses but fail to transmit acoustic information to the SGNs, leading to highly raised auditory thresholds. We also found that in adult Bai1-deficient mice, despite the almost complete absence of AMPA receptors, the SGN fibres innervating the IHCs did not degenerate. RNA sequencing and western blotting also indicate that AMPA receptors are expressed in the cochlea of Bai1-deficient mice, highlights that BAI1 is involved is trafficking or anchoring GluR2-4 to the PSDs. Moreover, these results have identified novel molecular and functional mechanisms required for sound encoding at cochlear ribbon synapses.

Published in

BAI1 localizes AMPA receptors at the cochlear afferent post-synaptic density and is essential for hearing

Carlton AJ, Jeng JY, Grandi FC et al. · Cell reports 2024 · PMID 38564333 · doi:10.1016/j.celrep.2024.114025

This dataset

Open GSE254269 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE254269_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1069109 and SRA study SRP486013. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38564333) ↗

Study design

7 × Bai1KO_P7_Het vs 7 × Bai1KO_P7_Homo vs 3 × Bai1KO_P22_Het vs 3 × Bai1KO_P22_Homo

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 20 sample titles; they account for 20 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.

Samples in this study

GSM8037043 Bai1KO_P22_Het_Rep1 Bai1KO_P22_Het
GSM8037044 Bai1KO_P22_Het_Rep2 Bai1KO_P22_Het
GSM8037045 Bai1KO_P22_Het_Rep3 Bai1KO_P22_Het
GSM8037046 Bai1KO_P22_Homo_Rep1 Bai1KO_P22_Homo
GSM8037047 Bai1KO_P22_Homo_Rep2 Bai1KO_P22_Homo
GSM8037048 Bai1KO_P22_Homo_Rep3 Bai1KO_P22_Homo
GSM8037049 Bai1KO_P7_Het_Rep1 Bai1KO_P7_Het
GSM8037050 Bai1KO_P7_Het_Rep2 Bai1KO_P7_Het
GSM8037051 Bai1KO_P7_Het_Rep3 Bai1KO_P7_Het
GSM8037052 Bai1KO_P7_Het_Rep4 Bai1KO_P7_Het
GSM8037053 Bai1KO_P7_Het_Rep5 Bai1KO_P7_Het
GSM8037054 Bai1KO_P7_Het_Rep6 Bai1KO_P7_Het
GSM8037055 Bai1KO_P7_Het_Rep7 Bai1KO_P7_Het
GSM8037056 Bai1KO_P7_Homo_Rep1 Bai1KO_P7_Homo
GSM8037057 Bai1KO_P7_Homo_Rep2 Bai1KO_P7_Homo
GSM8037058 Bai1KO_P7_Homo_Rep3 Bai1KO_P7_Homo
GSM8037059 Bai1KO_P7_Homo_Rep4 Bai1KO_P7_Homo
GSM8037060 Bai1KO_P7_Homo_Rep5 Bai1KO_P7_Homo
GSM8037061 Bai1KO_P7_Homo_Rep6 Bai1KO_P7_Homo
GSM8037062 Bai1KO_P7_Homo_Rep7 Bai1KO_P7_Homo

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