Bulk and single cell RNA-seq of MCF7 and MCF7 TDP2-KO cells treated with/without estrogen
Single-cell RNA-seq · human · 16 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 16 samples: 7 conditions, mostly in duplicateGroups 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
- TDP2 is a regulator of estrogen-responsive oncogene expressionNAR cancer · 2024
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 GSE225423_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA815369 and SRA study SRP420311. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 4 samples read as cases, 2 as controls.
How we read this: 7 replicated groups read from 16 sample titles; they account for 14 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.
- GSM7048318 MCF7 Parental Untreated bulk RNA-seq biological replicate 1
- GSM7048319 MCF7 Parental Untreated bulk RNA-seq biological replicate 2
- GSM7048320 MCF7 Parental E2-treated 2 hours bulk RNA-seq biological replicate 1 MCF7 Parental E2-treate…
- GSM7048321 MCF7 Parental E2-treated 2 hours bulk RNA-seq biological replicate 2 MCF7 Parental E2-treate…
- GSM7048322 MCF7 TDP2KO Untreated bulk RNA-seq biological replicate 1 MCF7 TDP2KO Untreated b…
- GSM7048323 MCF7 TDP2KO Untreated bulk RNA-seq biological replicate 2 MCF7 TDP2KO Untreated b…
- GSM7048324 MCF7 TDP2KO E2-treated 2 hours bulk RNA-seq biological replicate 1 MCF7 TDP2KO E2-treated …
- GSM7048325 MCF7 TDP2KO E2-treated 2 hours bulk RNA-seq biological replicate 2 MCF7 TDP2KO E2-treated …
- GSM7048326 MCF7 WT Untreated scRNA S1 MCF7 WT Untreated scRNA…
- GSM7048327 MCF7 WT 10 nM E2 treatment for 2h scRNA S2 MCF7 WT 10 nM E2 treatm…
- GSM7048328 MCF7 TDP2 knockout Untreated scRNA S3 MCF7 TDP2 knockout Untr…
- GSM7048329 MCF7 TDP2 knockout 10 nM E2 treatment for 2h scRNA S4 MCF7 TDP2 knockout 10 n…
- GSM7048330 MCF7 WT Untreated scRNA S5 MCF7 WT Untreated scRNA…
- GSM7048331 MCF7 WT 10 nM E2 treatment for 2h scRNA S6 MCF7 WT 10 nM E2 treatm…
- GSM7048332 MCF7 TDP2 knockout Untreated scRNA S7 MCF7 TDP2 knockout Untr…
- GSM7048333 MCF7 TDP2 knockout 10 nM E2 treatment for 2h scRNA S8 MCF7 TDP2 knockout 10 n…
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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.