CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression
RNA-seq (gene expression) · human · 108 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)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 108 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
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 GSE234328_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 PRJNA980750 and SRA study SRP441416. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 104 samples.
How we read this: 34 replicated groups read from 108 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.
- GSM7465007 HECT_MB-436_1_inter_30
- GSM7465008 HECT_MB-436_2_inter_30
- GSM7465009 HECT_MB-436_3_inter_30
- GSM7465010 HECT_MB-436_4_inter_30
- 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
+ 68 more — browse all 108 samples with per-sample file links →
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares progression
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
- GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing
- GSE276052 CRISPR screening identifies regulators of enhancer mediated androgen receptor transcription in advanced prostate cancer 92 samples shares crispr, identifies, screening
- GSE301632 Genome-wide CRISPR-Cas9 knockout screening identifies NUDCD2 depletion as sensitizer for bortezomib, carfilzomib and ixazomib in multiple myeloma. 27 samples shares crispr, identifies, screening
- GSE282326 CRISPR screening reveals that RNA helicase DDX41 triggers ribosome biogenesis and cancer progression through R-loop-mediated RPL/RPS transcription 25 samples shares crispr, progression, screening
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.