RNA-seq of MCF-7 cells with ER or FOXA1 knockout and/or GDC-9545 treatment
RNA-seq (gene expression) · human · 10 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
- 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE246363_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 PRJNA1032621 and SRA study SRP468649. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 10 sample titles: 10 distinct titles with little repetition. 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.
- GSM7867662 SAM24423296_MCF-7, RNP NTC, sg2, 4 days, rep1
- GSM7867663 SAM24423297_MCF-7, RNP NTC, sg2, 4 days, rep2
- GSM7867664 SAM24423298_MCF-7, RNP NTC, sg2 + 300nM GDC-9545 for 4 days, rep1
- GSM7867665 SAM24423299_MCF-7, RNP NTC, sg2 + 300nM GDC-9545 for 4 days, rep2
- GSM7867666 SAM24423300_MCF-7, RNP ESR1, sgAA 4 days, rep1
- GSM7867667 SAM24423301_MCF-7, RNP ESR1, sgAA 4 days, rep2
- GSM7867668 SAM24423302_MCF-7, RNP FoxA1, sgAC 4 days, rep1
- GSM7867669 SAM24423303_MCF-7, RNP FoxA1, sgAC 4 days, rep2
- GSM7867670 SAM24423304_MCF-7, RNP FoxA1, sgAC + 300nM GDC-9545 for 4 days, rep1
- GSM7867671 SAM24423305_MCF-7, RNP FoxA1, sgAC + 300nM GDC-9545 for 4 days, rep2
- GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares treatment, rna-seq
- GSE278450 Glioblastoma scRNA-seq shows treatment-induced, immune-dependent increase in mesenchymal cancer cells and structural variants in distal neural stem cells 22 samples shares treatment, rna-seq
- GSE180948 RNA-Seq based transcriptome analysis of colorectal cancer cells in response to lactate treatment 12 samples shares treatment, rna-seq
- GSE307843 Transcriptomic profiling in MCF7 parent and RB1 knockout cells following treatment with abemaciclib 12 samples shares treatment, knockout
- GSE285009 Mechanistic Investigation of Five Small-Molecule Inhibitors in the Treatment of Pemphigus Vulgaris via RNA-Seq Analysis 34 samples shares treatment, rna-seq
- GSE305389 Stromal and Endothelial Transcriptional Changes during Progression from MGUS to Myeloma and after Treatment Response [RNA-Seq] 25 samples shares treatment, rna-seq
- GSE338087 Patient tumor bulk RNA-seq analysis of the pre-axi-cel treatment tumor microenvironment in large B cell lymphoma 19 samples shares treatment, rna-seq
- GSE334189 RNA-seq analysis of global gene expression changes in human FSHD immortalized myotubes following treatment with the BAZ1A inhibitor C06 18 samples shares treatment, rna-seq
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.