GEO series
CRISPR-Enabled Profiling of Enhancer RNA-Producing Super-Enhancers in Triple-Negative Breast Cancer Identifies Drivers of Tumor Progression [RNA-Seq]
GSE234324
Homo sapiens (human)
RNA-seq (gene expression)
104 samples
Submitted 2024/08/14
Platform GPL24676
At a glance
RNA-seq (gene expression) · human · 104 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
- 104 samples: 34 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
- CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer ProgressionCancer research · 2024
Summary (written by the submitters)
Triple-negative breast cancer (TNBC) is the most therapeutically recalcitrant form of breast cancer. Pioneering genomic studies have identified the repertoire of expressed genes in the distinct molecular subtypes of breast cancer and have been instrumental in providing diagnostic, prognostic, and therapeutic guidance. Yet breast cancer remains the second leading cause of cancer mortality in women.
Read the full summary ↓
This is due, in part, to the paucity of targeted therapies for triple-negative breast cancer (TNBC). We posit that a systematic analysis of regulatory elements that extend beyond protein coding genes will lead to novel avenues for therapeutic intervention. To this end, we analyzed the regulatory mechanisms of TNBC-specific transcriptional enhancers together with their non-coding enhancer RNA (eRNA) transcripts. We systematically probed the functions of the top 30 eRNA-producing super-enhancers using a high-throughput CRISPR-interference (dCas9-KRAB) assay coupled to RNA-seq that enabled unbiased detection of target genes genome-wide. Utilizing Hi-C, we constructed 3D chromatin interaction maps to annotate direct target genes for each super-enhancer and highlight their proclivity for genes that portend worse clinical outcomes in TNBC patients. To illustrate the utility of this dataset, we selected a novel super-enhancer controlling the nearby PODXL gene and demonstrate that deletion of the super-enhancer (via Cas9 deletion) or specific degradation of its enhancer RNAs (via Cas13 RNA cleavage) leads to profound effects on target gene expression, cell proliferation, and migration. Furthermore, complete knockout of the PODXL super-enhancer leads to a significant decrease in tumor growth and metastatic potential in mouse xenograft experiments. Collectively, this work examines several fundamental questions about how regulatory information encoded into eRNA-producing super-enhancers drives gene expression networks that underlie the biology of triple-negative breast cancer.
Published in
Lewis MW, King CM, Wisniewska K et al.
· Cancer research 2024
· PMID 39186674
· doi:10.1158/0008-5472.CAN-23-3995
This dataset
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.
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 GSE234324_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA980829 and SRA study SRP441416. Searching any of these in the dataset finder brings you back here.
Study design
34 conditions, mostly in triplicate
Positive control CSF1 enhancer ×4
Positive control CSF1 gene promoter ×4
Super-enhancer 39 ×3
Super-enhancer 86 ×3
Super-enhancer 84 ×3
Super-enhancer 32 ×3
Super-enhancer 54 ×3
Super-enhancer 77 ×3
+26 more
Supports a between-group comparison across 104 samples.
How we read this: 34 replicated groups read from 104 sample titles; they account for 104 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
- GSM7465011 Super-enhancer 39 replicate 3 Super-enhancer 39
- GSM7465012 Super-enhancer 39 replicate 1 Super-enhancer 39
- GSM7465013 Super-enhancer 39 replicate 4 Super-enhancer 39
- GSM7465014 Super-enhancer 86 replicate 1 Super-enhancer 86
- GSM7465015 Super-enhancer 86 replicate 3 Super-enhancer 86
- GSM7465016 Super-enhancer 86 replicate 4 Super-enhancer 86
- GSM7465017 Super-enhancer 84 replicate 3 Super-enhancer 84
- GSM7465018 Super-enhancer 84 replicate 1 Super-enhancer 84
- GSM7465019 Super-enhancer 84 replicate 4 Super-enhancer 84
- GSM7465020 Super-enhancer 32 replicate 4 Super-enhancer 32
- GSM7465021 Super-enhancer 32 replicate 1 Super-enhancer 32
- GSM7465022 Super-enhancer 32 replicate 3 Super-enhancer 32
- GSM7465023 Positive control CSF1 enhancer replicate 4 Positive control CSF1 e…
- GSM7465024 Positive control CSF1 enhancer replicate 1 Positive control CSF1 e…
- GSM7465025 Positive control CSF1 enhancer replicate 3 Positive control CSF1 e…
- GSM7465026 Super-enhancer 54 replicate 4 Super-enhancer 54
- GSM7465027 Super-enhancer 54 replicate 1 Super-enhancer 54
- GSM7465028 Super-enhancer 54 replicate 3 Super-enhancer 54
- GSM7465029 Super-enhancer 77 replicate 1 Super-enhancer 77
- GSM7465030 Super-enhancer 77 replicate 3 Super-enhancer 77
- GSM7465031 Super-enhancer 77 replicate 4 Super-enhancer 77
- GSM7465032 Super-enhancer 52 replicate 3 Super-enhancer 52
- GSM7465033 Super-enhancer 52 replicate 1 Super-enhancer 52
- GSM7465034 Super-enhancer 52 replicate 4 Super-enhancer 52
- GSM7465035 Super-enhancer 83 replicate 1 Super-enhancer 83
- GSM7465036 Super-enhancer 30 replicate 4 Super-enhancer 30
- GSM7465037 Super-enhancer 30 replicate 3 Super-enhancer 30
- GSM7465038 Super-enhancer 83 replicate 3 Super-enhancer 83
- GSM7465039 Super-enhancer 30 replicate 1 Super-enhancer 30
- GSM7465040 Super-enhancer 66 replicate 3 Super-enhancer 66
- GSM7465041 Super-enhancer 66 replicate 1 Super-enhancer 66
- GSM7465042 Super-enhancer 66 replicate 4 Super-enhancer 66
- GSM7465043 Super-enhancer 9 replicate 4 Super-enhancer 9
- GSM7465044 Positive control CSF1 gene promoter replicate 1 Positive control CSF1 g…
- GSM7465045 Super-enhancer 9 replicate 1 Super-enhancer 9
- GSM7465046 Super-enhancer 9 replicate 3 Super-enhancer 9
- GSM7465047 Super-enhancer 69 replicate 1 Super-enhancer 69
- GSM7465048 Super-enhancer 69 replicate 3 Super-enhancer 69
- GSM7465049 Super-enhancer 69 replicate 4 Super-enhancer 69
- GSM7465050 Super-enhancer 71 replicate 4 Super-enhancer 71
+ 64 more — browse all 104 samples with per-sample file links →
Datasets on a similar topic
- GSE234328 CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression 108 samples shares super-enhancers, triple-negative, progression, identifies, enhancer, drivers
- GSE292717 Super-enhancers-driven SOX4/SMAD3 enhances AXL signaling via membrane phospholipid remodeling to accelerate leukemia progression [RNA-Seq] 42 samples shares super-enhancers, progression, enhancer
- GSE261988 SWI/SNF is a gatekeeper of chromatin access at enhancer networks controlling triple-negative breast cancer progression [ChIP-Seq] 79 samples shares triple-negative, progression, enhancer
- GSE261986 SWI/SNF is a gatekeeper of chromatin access at enhancer networks controlling triple-negative breats cancer progression [ATAC-seq] 36 samples shares triple-negative, progression, enhancer
- GSE292716 Super-enhancers-driven SOX4/SMAD3 enhances AXL signaling via membrane phospholipid remodeling to accelerate leukemia progression [ChIP-seq] 20 samples shares super-enhancers, progression, enhancer
- GSE292718 Super-enhancers-driven SOX4/SMAD3 enhances AXL signaling via membrane phospholipid remodeling to accelerate leukemia progression [CUT&Tag] 16 samples shares super-enhancers, progression, enhancer
- GSE334033 A Patient-Derived Xenograft Model Identifies AK1 as a Key Regulator of Metastatic Potential in Primary Triple-Negative Breast Cancer 105 samples shares triple-negative, identifies
- GSE256188 Super-enhancers reorganization controls re-sensitization of oxaliplatin-resistant FBXW7-mutated colorectal cancer 36 samples shares super-enhancers, enhancer
Share this dataset
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.