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Netrin1 patterns the dorsal spinal cord through modulation of Bmp signaling

GSE246903 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2024/04/23 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 16 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
Homo sapiens (human)
Samples
16 samples: 6 conditions, mostly in triplicateGroups 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
Netrin1 patterns the dorsal spinal cord through modulation of Bmp signalingbioRxiv : the preprint server for biology · 2023
Summary (written by the submitters)
We directed mESCs towards the dorsal sensory interneurons (dIs) using RA-/+ BMP4 and tested the effects of an axon guidance molecule netrin1 on dI differentiation in vitro. Using bulk-RNA seq analysis, we investiagted when the addition of netrin 1 will affect the transcriptome of differentiating dIs.
Read the full summary ↓
For this analysis, we used three timewindows (conditions 1-3) for netrin addition (1) condition 1 netrin 1 was added together with RA+BMP4 at day 4, and RNA seq was conducted at day 5, (2) netrin1 was added after the RA+BMP4 mediated patterning at day 5 and RNA seq was conducted at day 6, and (3) netrin1 was added for the extended duration between day 5-day9 to investigate the netrin1 effects throughout the dI differentiation and RNA seq was conducted at day 9. Through this analysis we identified that netrin1 downregulate BMP signaling pathway, possibly through modlulating the mRNA processing of key mediator of BMP signaling such as Id genes and BMP signaling inhibitor Smad7 and affect dI differentiation. This is the first report to show that netrin1 regulate dI fate specification in the dorsal spinal cord.
Published in
Netrin1 patterns the dorsal spinal cord through modulation of Bmp signaling
Alvarez S, Gupta S, Honeychurch K et al. · bioRxiv : the preprint server for biology 2023 · PMID 37961605 · doi:10.1101/2023.11.02.565384
This dataset
Open GSE246903 in finder → Find more human 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 GSE246903_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 PRJNA1035079 and SRA study SRP469935. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37961605) ↗
Study design
6 conditions, mostly in triplicate
mESCs, no netrin1 control (condition 1), ×3 mESCs, netrin1 treated samples (condition 1), ×3 mESCs, no netrin1 control (condition 2), ×3 mESCs, netrin1 treated samples (condition 2), ×3 mESCs, no netrin1 control (condition 3), ×2 mESCs, netrin1 treated samples (condition 3), ×2

Supports a case/control comparison: 8 samples read as cases, 8 as controls.

How we read this: 6 replicated groups read from 16 sample titles; they account for 16 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
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