Cancer-stromal cell interactions in breast cancer brain metastases induce glycocalyx-mediated resistance to HER2-targeting therapies [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Samples
- 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups 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
- Cancer-stromal cell interactions in breast cancer brain metastases induce glycocalyx-mediated resistance to HER2-targeting therapiesProceedings of the National Academy of Sciences of the United States of America · 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 GSE249459_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1049323 and SRA study SRP476115. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 24 sample titles: 24 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.
- GSM7948478 453_DMSO_1 (ATAC-seq)
- GSM7948479 453_DMSO_2 (ATAC-seq)
- GSM7948480 453_NER_1 (ATAC-seq)
- GSM7948481 453_NER_2 (ATAC-seq)
- GSM7948482 453plusBM3_DMSO_1 (ATAC-seq)
- GSM7948483 453plusBM3_DMSO_2 (ATAC-seq)
- GSM7948484 453plusBM3_NER_1 (ATAC-seq)
- GSM7948485 453plusBM3_NER_2 (ATAC-seq)
- GSM7948486 s1_HCC1954_mC+_DMSO_A_MAG1 (ATAC-seq)
- GSM7948487 s5_HCC1954BM3__mC+_DMSO_B_MAG10 (ATAC-seq)
- GSM7948488 s5_HCC1954BM3_GFP+_DMSO_A_MAG11 (ATAC-seq)
- GSM7948489 s5_HCC1954BM3_GFP+_DMSO_B_MAG12 (ATAC-seq)
- GSM7948490 s6_HCC1954BM3_mC+_NER_A_MAG13 (ATAC-seq)
- GSM7948491 s6_HCC1954BM3_mC+_NER_B_MAG14 (ATAC-seq)
- GSM7948492 s6_HCC1954BM3_GFP+_NER_A_MAG15 (ATAC-seq)
- GSM7948493 s6_HCC1954BM3_GFP+_NER_B_MAG16 (ATAC-seq)
- GSM7948494 s1_HCC1954_mC+_DMSO_B_MAG2 (ATAC-seq)
- GSM7948495 s2_HCC1954_mC+_NER_A_MAG3 (ATAC-seq)
- GSM7948496 s2_HCC1954_mC+_NER_B_MAG4 (ATAC-seq)
- GSM7948497 s3_BM3_GFP+_DMSO_A_MAG5 (ATAC-seq)
- GSM7948498 s3_BM3_GFP+_DMSO_B_MAG6 (ATAC-seq)
- GSM7948499 s4_BM3_GFP+_NER_A_MAG7 (ATAC-seq)
- GSM7948500 s4_BM3_GFP+_NER_B_MAG8 (ATAC-seq)
- GSM7948501 s5_HCC1954BM3_mC+_DMSO_A_MAG9 (ATAC-seq)
- GSE299923 Distinct interactions between pioneer factor Ascl1/E12a and nucleosomes drive cell fate transitions [ATAC-seq] 39 samples shares interactions, atac-seq
- GSE274484 The Long Non-coding RNA Lnc-RAINY Regulates Genes Involved in Radiation Susceptibility Through DNA:DNA:RNA triplex-forming Interactions and has Tumor Therapeutic Potential in Non-small Cell Lung Cancers [ATAC-seq] 16 samples shares interactions, atac-seq
- GSE271752 Macromolecular interactions dictate Polycomb-mediated epigenetic repression [ChIP-seq] 194 samples shares interactions
- GSE299971 Distinct interactions between pioneer factor Ascl1/E12a and nucleosomes drive cell fate transitions 63 samples shares interactions
- GSE263637 CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation [ChIPmentation] 42 samples shares interactions
- GSE300854 Collective unstructured interactions drive chromatin binding of transcription factors. [CUT&RUN] 40 samples shares interactions
- GSE299920 Distinct interactions between pioneer factor Ascl1/E12a and nucleosomes drive cell fate transitions [ChIP-seq] 24 samples shares interactions
- GSE278607 Virus-Human Chromatin Interactions Reorganise 3D Genome and Hijack KDM5B for Promoting Metastasis in Nasopharyngeal Carcinoma [CUT&RUN-seq] 18 samples shares interactions
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.