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Effect of CRY2 stabilizer and proteasome inhibitor on the transcription of MDA-MB-231 cells [RNA-seq]

GSE266011 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2024/06/12 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 36 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
36 samples: 12 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
Targeting circadian transcriptional programs through a cis-regulatory mechanism in triple negative breast cancerbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
In this study we tested if the transcriptional activity of circadian transcription factors, BMAL1 and CLOCK, can be repressed by small molecules in triple negative breast cancer cells. We validated that CRY inhibitors and proteasome inhibitors synergize and can recapitulate the phenotype of genetic knockdown of BMAL1 and CLOCK. To investigate the potential mechanism of the effect of this drug combination, we performed RNA sequencing analysis on cells treated with either single drug or drug combination at different time points.
Published in
Targeting circadian transcriptional programs through a cis-regulatory mechanism in triple negative breast cancer
Pan Y, Chiu TP, Zhou L et al. · bioRxiv : the preprint server for biology 2024 · PMID 38746115 · doi:10.1101/2024.04.26.590360
This dataset
Open GSE266011 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 GSE266011_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 PRJNA1105320 and SRA study SRP504374. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38746115) ↗
Study design
12 conditions, mostly in triplicate
MDA-MB-231, MG_combination_DMSO-treated, 8-ho… ×3 MDA-MB-231, MG_combination_SHP1705-treated, 8… ×3 MDA-MB-231, MG_combination_MG132-treated, 8-h… ×3 MDA-MB-231, MG_combination_drug combination-t… ×3 MDA-MB-231, CFZ_combination_DMSO-treated, 8-h… ×3 MDA-MB-231, CFZ_combination_SHP1705-treated, … ×3 MDA-MB-231, CFZ_combination_CFZ-treated, 8-ho… ×3 MDA-MB-231, CFZ_combination_drug combination-… ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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
Datasets on a similar topic

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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.