Androgen receptor programming in human tissue implicates HOXB13 in prostate pathogenesis [ChIP-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 29 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
- 29 samples: 13 × Patient AR prostate tumor tissue vs 7 × Patient prostate normal tissue vs 2 × AR Chip-seq_LHSAR_FOXA1_HOXB13 vs 2 × AR Chip-seq_LHSAR_LacZGroups 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 GSE56288_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 PRJNA242853 and SRA study SRP040649. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 4 replicated groups read from 29 sample titles; they account for 24 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.
- GSM1358395 Patient prostate normal tissue 1 Patient prostate normal…
- GSM1358396 Patient AR prostate tumor tissue 2 Patient AR prostate tum…
- GSM1358397 Patient prostate normal tissue 3 Patient prostate normal…
- GSM1358398 Patient AR prostate tumor tissue 4 Patient AR prostate tum…
- GSM1358399 Patient prostate normal tissue 5 Patient prostate normal…
- GSM1358400 Patient AR prostate tumor tissue 6 Patient AR prostate tum…
- GSM1358401 Patient prostate normal tissue 7 Patient prostate normal…
- GSM1358402 Patient prostate normal tissue 8 Patient prostate normal…
- GSM1358403 Patient AR prostate tumor tissue 9 Patient AR prostate tum…
- GSM1358404 Patient AR prostate tumor tissue 10 Patient AR prostate tum…
- GSM1358405 Patient prostate normal tissue 11 Patient prostate normal…
- GSM1358406 Patient AR prostate tumor tissue 12 Patient AR prostate tum…
- GSM1358407 Patient AR prostate tumor tissue 13 Patient AR prostate tum…
- GSM1358408 Patient AR prostate tumor tissue 14 Patient AR prostate tum…
- GSM1358409 Patient prostate normal tissue 15 Patient prostate normal…
- GSM1358410 Patient AR prostate tumor tissue 16 Patient AR prostate tum…
- GSM1358411 Patient AR prostate tumor tissue 17 Patient AR prostate tum…
- GSM1358412 Patient AR prostate tumor tissue 18 Patient AR prostate tum…
- GSM1358413 Patient AR prostate tumor tissue 19 Patient AR prostate tum…
- GSM1358414 Patient AR prostate tumor tissue 20 Patient AR prostate tum…
- GSM1716762 FOXA1 Chip-seq_tumor
- GSM1716763 HOXB13 Chip-seq_tumor
- GSM1716764 HOXB13 Chip-seq_LNCaP
- GSM1716765 AR Chip-seq_LHSAR_FOXA1
- GSM1716766 AR Chip-seq_LHSAR_HOXB13
- GSM1716767 AR Chip-seq_LHSAR_FOXA1_HOXB13_1 AR Chip-seq_LHSAR_FOXA1…
- GSM1716768 AR Chip-seq_LHSAR_FOXA1_HOXB13_2 AR Chip-seq_LHSAR_FOXA1…
- GSM1716769 AR Chip-seq_LHSAR_LacZ_1 AR Chip-seq_LHSAR_LacZ
- GSM1716770 AR Chip-seq_LHSAR_LacZ_2 AR Chip-seq_LHSAR_LacZ
- GSE239270 Investigate FOXA2, NKX2-1, CTCF and P300 cistrome and enhancer (H3K27ac and H3k4me1) reprogramming during NEPC transformation by ChIP-seq. 104 samples shares programming, chip-seq
- GSE206726 Epigenetic reprogramming of the mesenchymal state by SUV39H1/H2 [ChIP-Seq] 42 samples shares programming, chip-seq
- GSE311971 Regulation of lineage reprogramming by dynamic chromatin SUMOylation (ChIP-seq) 41 samples shares programming, chip-seq
- GSE261321 NF-κB- and TET2-mediated macrophage reprogramming overrides the anti-inflammatory effects of hypoxia and improves responses in human cancer ChIP-Seq). 24 samples shares programming, chip-seq
- GSE308983 Reprogramming lineage features promotes epithelial behavior in carcinoma cells [ChIP-Seq] 23 samples shares programming, chip-seq
- GSE236589 Enhancer reprogramming underlies therapeutic utility of a SMARCA2 degrader in SMARCA4 mutant cancer [ChIP-Seq] 12 samples shares programming, chip-seq
- GSE279497 G-quadruplex structures regulate long-range transcriptional reprogramming to promote drug resistance in ovarian cancer [ChIP-seq] 12 samples shares programming, chip-seq
- GSE181389 Transcriptome profiling of HOXA13 and HOXB13 expression knockdown in bladder cancer cell lines. 59 samples shares hoxb13
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.