miRNA-seq and RNA-seq profiles of breast cancer cell lines
Non-coding RNA profiling · human · 79 samples
- What it is
- Non-coding RNA profilingLevels of RNAs that do not code for proteins, such as miRNA or lncRNA.
- Organism
- Homo sapiens (human)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 79 samples: 65 distinct titles, 7 of them repeatedGroups 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 GSE237728_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.
Also filed as BioProject PRJNA996501 and SRA study SRP447928. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 79 sample titles: 65 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.
- GSM7575764 SUM159PT_CTRL_1_cells expressing the negative control sgRNA_1
- GSM7575765 SUM159PT_CTRL_2_cells expressing the negative control sgRNA_2
- GSM7575766 SUM159PT_CTRL_3_cells expressing the negative control sgRNA_3
- GSM7575767 SUM159PT_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1
- GSM7575768 SUM159PT_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2
- GSM7575769 SUM159PT_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3
- GSM7575770 BT-549_CTRL_1_cells expressing the negative control sgRNA_1
- GSM7575771 BT-549_CTRL_2_cells expressing the negative control sgRNA_2
- GSM7575772 BT-549_CTRL_3_cells expressing the negative control sgRNA_3
- GSM7575773 BT-549_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1
- GSM7575774 BT-549_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2
- GSM7575775 BT-549_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3
- GSM7575776 MDA-MB-231_CTRL_1_cells expressing the negative control sgRNA_1
- GSM7575777 MDA-MB-231_CTRL_2_cells expressing the negative control sgRNA_2
- GSM7575778 MDA-MB-231_CTRL_3_cells expressing the negative control sgRNA_3
- GSM7575779 MDA-MB-231_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1
- GSM7575780 MDA-MB-231_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2
- GSM7575781 MDA-MB-231_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3
- GSM7575782 MDA-MB-436_CTRL_1_cells expressing the negative control sgRNA_1
- GSM7575783 MDA-MB-436_CTRL_2_cells expressing the negative control sgRNA_2
- GSM7575784 MDA-MB-436_CTRL_3_cells expressing the negative control sgRNA_3
- GSM7575785 MDA-MB-436_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1
- GSM7575786 MDA-MB-436_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2
- GSM7575787 MDA-MB-436_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3
- GSM7575788 MCF-7_CTRL_1_cells expressing the negative control sgRNA_1
- GSM7575789 MCF-7_CTRL_2_cells expressing the negative control sgRNA_2
- GSM7575790 MCF-7_CTRL_3_cells expressing the negative control sgRNA_3
- GSM7575791 MCF-7_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1
- GSM7575792 MCF-7_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2
- GSM7575793 MCF-7_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3
- GSM7575794 T47D_CTRL_1_cells expressing the negative control sgRNA_1
- GSM7575795 T47D_CTRL_2_cells expressing the negative control sgRNA_2
- GSM7575796 T47D_CTRL_3_cells expressing the negative control sgRNA_3
- GSM7575797 T47D_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1
- GSM7575798 T47D_ZSWIM8_KD_2_cells expressing the ZSWIM targeting sgRNA_2
- GSM7575799 T47D_ZSWIM8_KD_3_cells expressing the ZSWIM targeting sgRNA_3
- GSM7575800 SK-BR-3_CTRL_1_cells expressing the negative control sgRNA_1
- GSM7575801 SK-BR-3_CTRL_2_cells expressing the negative control sgRNA_2
- GSM7575802 SK-BR-3_CTRL_3_cells expressing the negative control sgRNA_3
- GSM7575803 SK-BR-3_ZSWIM8_KD_1_cells expressing the ZSWIM targeting sgRNA_1
+ 39 more — browse all 79 samples with per-sample file links →
- 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 · shares breast
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing · shares breast
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares breast
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares breast
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares rna-seq, breast
- GSE294300 Single-cell gene expression profiles of cells from primary colorectal cancer and adjacent normal tissue [scRNA-Seq] 36 samples shares profiles, rna-seq
- GSE261713 Linking single cell genomes and transcriptomes at scale to decode breast cancer progression [scRNA-seq] 35 samples shares rna-seq, breast
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.