X-Linked Cancer-Associated Polypeptide, Encoded by a Putative Noncoding RNA, Regulates Gene Expression and Cellular Pathways in Breast Cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 55 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)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 55 samples: 14 conditions, mostly in duplicateGroups 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
- X-linked cancer-associated polypeptide (XCP) from lncRNA1456 modulates PHF8 histone demethylase activity to regulate the epigenome, gene expression, and cellular pathways in breast cancerOncogene · 2026
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 GSE288983_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 PRJNA1220153 and SRA study SRP558351. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 48 samples.
How we read this: 14 replicated groups read from 55 sample titles; they account for 48 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.
- GSM8745525 MCF-7 Input
- GSM8745526 MCF-7 Control KD Rep1, PHF8 ChIP
- GSM8745527 MCF-7 Control KD Rep2, PHF8 ChIP
- GSM8745528 MCF-7 1456 KD-1 Rep1, PHF8 ChIP
- GSM8745529 MCF-7 1456 KD-1 Rep2, PHF8 ChIP
- GSM8745530 MCF-7 1456 KD-2 Rep1, PHF8 ChIP
- GSM8745531 MCF-7 1456 KD-2 Rep2, PHF8 ChIP
- GSM8777111 MCF-7 GFP 1 MCF-7 GFP
- GSM8777112 MCF-7 GFP 2 MCF-7 GFP
- GSM8777113 MCF-7 GFP 3 MCF-7 GFP
- GSM8777114 MCF-7 GFP 4 MCF-7 GFP
- GSM8777115 MCF-7 GFP 5 MCF-7 GFP
- GSM8777116 MCF-7 GFP 6 MCF-7 GFP
- GSM8777117 MCF-7 GFP 7 MCF-7 GFP
- GSM8777118 MCF-7 GFP 8 MCF-7 GFP
- GSM8777119 MCF-7 XCP 1 MCF-7 XCP
- GSM8777120 MCF-7 XCP 2 MCF-7 XCP
- GSM8777121 MCF-7 XCP 3 MCF-7 XCP
- GSM8777122 MCF-7 XCP 4 MCF-7 XCP
- GSM8777123 MDA-MB-231 GFP 1 MDA-MB-231 GFP
- GSM8777124 MDA-MB-231 GFP 2 MDA-MB-231 GFP
- GSM8777125 MDA-MB-231 GFP 3 MDA-MB-231 GFP
- GSM8777126 MDA-MB-231 GFP 4 MDA-MB-231 GFP
- GSM8777127 MDA-MB-231 GFP 5 MDA-MB-231 GFP
- GSM8777128 MDA-MB-231 GFP 6 MDA-MB-231 GFP
- GSM8777129 MDA-MB-231 GFP 7 MDA-MB-231 GFP
- GSM8777130 MDA-MB-231 GFP 8 MDA-MB-231 GFP
- GSM8777131 MDA-MB-231 XCP 1 MDA-MB-231 XCP
- GSM8777132 MDA-MB-231 XCP 2 MDA-MB-231 XCP
- GSM8777133 MDA-MB-231 XCP 3 MDA-MB-231 XCP
- GSM8777134 MDA-MB-231 XCP 4 MDA-MB-231 XCP
- GSM8777135 MDA-MB-231 XCP 5 MDA-MB-231 XCP
- GSM8777136 MDA-MB-231 XCP 6 MDA-MB-231 XCP
- GSM8777137 MDA-MB-231 XCP 7 MDA-MB-231 XCP
- GSM8777138 MDA-MB-231 XCP 8 MDA-MB-231 XCP
- GSM8777139 MCF-7, GFP, Control KD Rep1 MCF-7, GFP, Control KD
- GSM8777140 MCF-7, GFP, Control KD Rep2 MCF-7, GFP, Control KD
- GSM8777141 MCF-7, GFP, lncRNA1456 KD set1 Rep1 MCF-7, GFP, lncRNA1456 …
- GSM8777142 MCF-7, GFP, lncRNA1456 KD set1 Rep2 MCF-7, GFP, lncRNA1456 …
- GSM8777143 MCF-7, GFP, lncRNA1456 KD set2 Rep1 MCF-7, GFP, lncRNA1456 …
+ 15 more — browse all 55 samples with per-sample file links →
- 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
- 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
- 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
- GSE288868 X-Linked Cancer-Associated Polypeptide, Encoded by a Putative Noncoding RNA, Regulates Gene Expression and Cellular Pathways in Breast Cancer [RNA-seq] 48 samples shares cancer-associated, polypeptide, noncoding, x-linked, putative, cellular, encoded, breast
- GSE256420 Long Noncoding VIM-AS1: Biomarker of Breast Fibrosis Susceptibility After Radiation Therapy and Promoter of Transforming Growth Factor Beta1–Driven Fibrosis 27 samples shares noncoding, breast
- GSE286577 Cancer-associated snaR-A noncoding RNA interacts with core splicing machinery and disrupts processing of mRNA subpopulations II 24 samples shares cancer-associated, noncoding
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.