Lineage specific chromatin modification guides Pax5 mediated gene expression in neuroendocrine like differentiation of prostate cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 32 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
- Prostate cancerThis series is part of our curated briefing on it.
- Samples
- 32 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
- Understanding the function of Pax5 in development of docetaxel-resistant neuroendocrine-like prostate cancersCell death & disease · 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 GSE210848_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 PRJNA867703 and SRA study SRP390737. 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 32 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.
- GSM6439110 ATAC-Seq C4-2B-1 ATAC-Seq C4-2B
- GSM6439111 ATAC-Seq C4-2B-2 ATAC-Seq C4-2B
- GSM6439112 ATAC-Seq C4-2B_Enza_Resist-1 ATAC-Seq C4-2B_Enza_Res…
- GSM6439113 ATAC-Seq C4-2B_Enza_Resist-2 ATAC-Seq C4-2B_Enza_Res…
- GSM6439116 1_C4-2BH3K18Ac_S1
- GSM6439117 2_C4-2BH3K18Ac_S2
- GSM6439118 3_C4-2BERH3K18Ac_S3
- GSM6439119 4_C4-2BERH3K18Ac_S4
- GSM6439120 5_C42B_H3K27Ac_S1
- GSM6439121 6_C42B_H3K27Ac_S2
- GSM6439122 7_C42BERH3K27Ac_S3
- GSM6439123 8_C42BERH3K27Ac_S4
- GSM6439124 13_C42B_Input_S5
- GSM6439125 14_C42BER-Input_S7
- GSM6439126 RNA-Seq C4-2B-1 RNA-Seq C4-2B
- GSM6439127 RNA-Seq C4-2B-2 RNA-Seq C4-2B
- GSM6439128 RNA-Seq C4-2B-3 RNA-Seq C4-2B
- GSM6439129 RNA-Seq C4-2BER-1 RNA-Seq C4-2BE
- GSM6439130 RNA-Seq C4-2BER-2 RNA-Seq C4-2BE
- GSM6439131 RNA-Seq C4-2BER-3 RNA-Seq C4-2BE
- GSM6439132 RNA-Seq DKD_scr1 RNA-Seq DKD_sc
- GSM6439133 RNA-Seq DKD_scr2 RNA-Seq DKD_sc
- GSM6439134 RNA-Seq DKD_scr3 RNA-Seq DKD_sc
- GSM6439135 RNA-Seq DKD_siPax5_1 RNA-Seq DKD_siPax5
- GSM6439136 RNA-Seq DKD_siPax5_2 RNA-Seq DKD_siPax5
- GSM6439137 RNA-Seq DKD_siPax5_3 RNA-Seq DKD_siPax5
- GSM6439138 RNA-Seq ER_scr1 RNA-Seq ER_sc
- GSM6439139 RNA-Seq ER_scr2 RNA-Seq ER_sc
- GSM6439140 RNA-Seq ER_scr3 RNA-Seq ER_sc
- GSM6439141 RNA-Seq ER_SiPax5_1 RNA-Seq ER_SiPax5
- GSM6439142 RNA-Seq ER_SiPax5_2 RNA-Seq ER_SiPax5
- GSM6439143 RNA-Seq ER_SiPax5_3 RNA-Seq ER_SiPax5
- GSE115501 RNA sequencing on circulating tumor cells from prostate cancer patients 136 samples same disease briefing · shares prostate
- GSE222467 The RNA binding proteins LARP4A and LARP4B promote tumour growth and metastasis in prostate cancer and osteosarcoma 12 samples same disease briefing · shares prostate
- GSE300947 A novel six-biomarker panel identified from male breast cancer-associated fibroblasts demonstrates prognostic power for prostate tumors 6 samples same disease briefing · shares prostate
- GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing · shares prostate
- GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
- GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing
- GSE328578 CBFA2T3-GLIS2 fusion-mediated mSWI/SNF chromatin remodeler disruption generates cancer-specific dependencies in AMKL 156 samples shares chromatin, specific, mediated
- GSE302864 DNMT3B drives neuroendocrine lineage plasticity and aggressive progression in prostate cancer 12 samples shares neuroendocrine, prostate, lineage
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.