Comparative RNA-seq analysis of PM2.5 responses in wildtype and malignantly transformed mouse mammary epithelial cells cultured as spheroids
RNA-seq (gene expression) · mouse · 8 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
- 8 samples: 2 × EpH4_3D_Control vs 2 × EpH4_3D_PM_treatment vs 2 × EpH4-AS_3D_Control vs 2 × EpH4-AS_3D_PM_treatmentGroups 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.
Read the full summary ↓
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 GSE337004_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 PRJNA1483692 and SRA study SRP713615. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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.
- GSM9846575 EpH4_3D_Control_1 EpH4_3D_Control
- GSM9846576 EpH4_3D_Control_2 EpH4_3D_Control
- GSM9846577 EpH4_3D_PM_treatment_1 EpH4_3D_PM_treatment
- GSM9846578 EpH4_3D_PM_treatment_2 EpH4_3D_PM_treatment
- GSM9846579 EpH4-AS_3D_Control_1 EpH4-AS_3D_Control
- GSM9846580 EpH4-AS_3D_Control_2 EpH4-AS_3D_Control
- GSM9846581 EpH4-AS_3D_PM_treatment_1 EpH4-AS_3D_PM_treatment
- GSM9846582 EpH4-AS_3D_PM_treatment_2 EpH4-AS_3D_PM_treatment
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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.