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mRNA sequencing of MDA-MB-231 engineered for doxycycline-inducible overexpression of wild-type or mutant myocardin related transcription factor A

GSE253047 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/10/10 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 24 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
24 samples: 8 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
mDia2 is an important mediator of MRTF-A-dependent regulation of breast cancer cell migrationMolecular biology of the cell · 2024
Summary (written by the submitters)
Myocardin Related Transcription Factor A (MRTF-A), a co-factor or serum response factor (SRF), has been implicated in breast cancer cell migration and metastatic potential. The goal of this sequencing effort was to determine which mRNA were regulated by MRTF-A overexpression and which mRNA were differentially regulated when function-inhibited (SAP-domain deleted or SRF-binding deficient) mutant MRTF-A were overexpressed.
Read the full summary ↓
GFP and luciferase expressing MDA-MB-231 cells engineered with doxycycline inducible overexpression of wild-type or mutant MRTF-A were treated with doxycycline for 72 hours prior to RNA collection. Two mutant versions of MRTF-A were used 1) a SAP-domain deleted mutant (deleted base-pairs 343-378) and 2) an SRF binding deficient mutant (mutated K237A, Y238A, H239A, Y241A). The cells were plated in a tissue-treated culture dish or on top of matrigel during doxycycline induction. RNA was extracted using the Qiagen RNeasy Plus Mini Kit according the manufacturer's instructions. Libraries were obtained starting from total RNA following the Illumina Stranded Total RNA preparation Ligation with Ribo-Zero Plus protocol. mRNA was then sequenced on the Illumina NextSeq2000.
Published in
mDia2 is an important mediator of MRTF-A-dependent regulation of breast cancer cell migration
Eder I, Yu V, Antonello J et al. · Molecular biology of the cell 2024 · PMID 39196658 · doi:10.1091/mbc.E24-01-0008
This dataset
Open GSE253047 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 GSE253047_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 PRJNA1055029 and SRA study SRP479137. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39196658) ↗
Study design
8 conditions, mostly in triplicate
2D MDA-MB-231 Control ×3 2D MDA-MB-231 WT MRTF-A OX ×3 2D MDA-MB-231 dSAP MRTF-A OX ×3 2D MDA-MB-231 dSRF MRTF-A OX ×3 3D MDA-MB-231 Control ×3 3D MDA-MB-231 WT MRTF-A OX ×3 3D MDA-MB-231 dSAP MRTF-A OX ×3 3D MDA-MB-231 dSRF MRTF-A OX ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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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