Molecular Portraits of Social Adversity in Breast Cancer [RNA-Seq]
RNA-seq (gene expression) · human · 66 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
- 66 samples: 33 × BCG vs 32 × BSSGroups 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
- Molecular Portraits of Social Adversity in Breast Cancer: Neighborhood Disadvantage Is Associated with Epigenetic Deregulation of Key Oncogenic PathwaysCancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2025
Read the full summary ↓
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 GSE290733_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 PRJNA1229680 and SRA study SRP566941. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 65 samples.
How we read this: 2 replicated groups read from 66 sample titles; they account for 65 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.
- GSM8820814 BSSR0553 BSS
- GSM8820815 BSSR0542 BSS
- GSM8820816 BSSR0624 BSS
- GSM8820817 BSSR0740 BSS
- GSM8820818 BSSR0727 BSS
- GSM8820819 BSSR0743 BSS
- GSM8820820 BSSR0754 BSS
- GSM8820821 BSSR0634 BSS
- GSM8820822 BSSR0551 BSS
- GSM8820823 BSSR0558 BSS
- GSM8820824 BSSR0567 BSS
- GSM8820825 BSSR0680 BSS
- GSM8820826 BSSR0738 BSS
- GSM8820827 BSSR0779 BSS
- GSM8820828 BSSR0997 BSS
- GSM8820829 BSSR1017 BSS
- GSM8820830 BSSR1030 BSS
- GSM8820831 BSSR1118 BSS
- GSM8820832 BSSR1123 BSS
- GSM8820833 BSSR1131 BSS
- GSM8820834 BSSR1153 BSS
- GSM8820835 BSSR1186 BSS
- GSM8820836 BSSR1297 BSS
- GSM8820837 BSSR1378 BSS
- GSM8820838 BSSR1390 BSS
- GSM8820839 BCG-006 BCG
- GSM8820840 BCG-023 BCG
- GSM8820841 BCG-026 BCG
- GSM8820842 BCG-036 BCG
- GSM8820843 BCG-047 BCG
- GSM8820844 BCG-148 BCG
- GSM8820845 BCG-155 BCG
- GSM8820846 BCG-164 BCG
- GSM8820847 BCG-209 BCG
- GSM8820848 BCG-228 BCG
- GSM8820849 BCG-254 BCG
- GSM8820850 BCG-310 BCG
- GSM8820851 BCG-379 BCG
- GSM8820852 BCG-390 BCG
- GSM8820853 BCG-400 BCG
+ 26 more — browse all 66 samples with per-sample file links →
- 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
- GSE261713 Linking single cell genomes and transcriptomes at scale to decode breast cancer progression [scRNA-seq] 35 samples shares rna-seq, breast
- GSE303346 Single-Cell RNA-Seq Reveals Immunosuppressive Effects of Triple-Negative Breast Cancer–Derived Exosomes on NK Cell Responses 16 samples shares rna-seq, breast
- GSE245414 RNA-seq profiling of breast metastases from different sites 42 samples shares rna-seq, breast
- GSE270680 A spatially resolved atlas of gastric cancer characterises a lymphocyte aggregated region [scRNA-seq] 77 samples shares rna-seq
- GSE292858 RNA-Seq analysis of tumor and matched normal samples from colorectal cancer patients. 73 samples shares rna-seq
- GSE222556 Neoadjuvant PARPi or Chemotherapy in Ovarian Cancer Informs Targeting Effector Treg Cells for Homologous-Recombination-Deficient Tumors [10x scRNA-seq] 67 samples shares rna-seq
- GSE269877 Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway 38 samples shares 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.