Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer [RNA-seq]
RNA-seq (gene expression) · human · 22 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
- 22 samples: 8 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
- Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancerNature cancer · 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 GSE253744_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 PRJNA1066856 and SRA study SRP484766. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 22 samples.
How we read this: 8 replicated groups read from 22 sample titles; they account for 22 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.
- GSM8027304 MDA-MB231, Ctrl, Day2,rep1 MDA-MB231, Ctrl, Day2,
- GSM8027305 MDA-MB231, Ctrl, Day2,rep2 MDA-MB231, Ctrl, Day2,
- GSM8027306 MDA-MB231, Nexturastat A, Day2,rep1 MDA-MB231, Nexturastat …
- GSM8027307 MDA-MB231, Nexturastat A, Day2,rep2 MDA-MB231, Nexturastat …
- GSM8027308 MDA-MB231, shCtrl, Day0,rep1 MDA-MB231, shCtrl, Day0,
- GSM8027309 MDA-MB231, shCtrl, Day0,rep2 MDA-MB231, shCtrl, Day0,
- GSM8027310 MDA-MB231, shCtrl, Day0,rep3 MDA-MB231, shCtrl, Day0,
- GSM8027311 MDA-MB231, shHDAC6-1, Day0,rep1 MDA-MB231, shHDAC6-1, D…
- GSM8027312 MDA-MB231, shHDAC6-1, Day0,rep2 MDA-MB231, shHDAC6-1, D…
- GSM8027313 MDA-MB231, shHDAC6-1, Day0,rep3 MDA-MB231, shHDAC6-1, D…
- GSM8027314 MDA-MB231, shHDAC6-2, Day0,rep1 MDA-MB231, shHDAC6-2, D…
- GSM8027315 MDA-MB231, shHDAC6-2, Day0,rep2 MDA-MB231, shHDAC6-2, D…
- GSM8027316 MDA-MB231, shHDAC6-2, Day0,rep3 MDA-MB231, shHDAC6-2, D…
- GSM8027317 MDA-MB231, DMSO, Day2,rep1 MDA-MB231, DMSO, Day2,
- GSM8027318 MDA-MB231, DMSO, Day2,rep2 MDA-MB231, DMSO, Day2,
- GSM8027319 MDA-MB231, DMSO, Day2,rep3 MDA-MB231, DMSO, Day2,
- GSM8027320 MDA-MB231, HPOB, Day2,rep1 MDA-MB231, HPOB, Day2,
- GSM8027321 MDA-MB231, HPOB, Day2,rep2 MDA-MB231, HPOB, Day2,
- GSM8027322 MDA-MB231, HPOB, Day2,rep3 MDA-MB231, HPOB, Day2,
- GSM8027323 MDA-MB231, TSA, Day2,rep1 MDA-MB231, TSA, Day2,
- GSM8027324 MDA-MB231, TSA, Day2,rep2 MDA-MB231, TSA, Day2,
- GSM8027325 MDA-MB231, TSA, Day2,rep3 MDA-MB231, TSA, Day2,
- GSE253743 Phase separation of phospho-HDAC6 drives aberrant chromatin architecture in triple-negative breast cancer [ChIP-seq, Cut&Tag, ATAC-seq] 41 samples shares triple-negative, phospho-hdac6, architecture, separation, chromatin, aberrant, drives
- GSE296212 LINE-1 locus transcription nucleates oncogenic chromatin architecture [RNA-Seq] 80 samples shares architecture, chromatin, rna-seq
- GSE337246 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [scRNA-Seq organoids] 35 samples shares architecture, chromatin, rna-seq
- GSE273681 NDF-FACT phase separation condensates are required for RNA Polymerase II transcription elongation through chromatin [RNA-Seq] 12 samples shares separation, chromatin, rna-seq
- GSE205248 H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs [scRNA-seq] 11 samples shares architecture, chromatin, rna-seq
- GSE322943 Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes [RNA-Seq] 100 samples shares architecture, rna-seq
- GSE275395 Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration (RNA-Seq) 30 samples shares architecture, rna-seq
- GSE324453 Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes [snRNA-Seq] 28 samples shares architecture, 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.