TWEAK/Fn14 signalling in Breast Cancer (Fn14 KO TNBC H3K27ac ChIP-seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 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
- 16 samples: 8 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
- TWEAK/Fn14 signalling driven super-enhancer reprogramming promotes pro-metastatic metabolic rewiring in triple-negative breast cancerNature communications · 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 GSE251866_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 PRJNA1055575 and SRA study SRP479518. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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.
- GSM7989287 MB231_control_K27_UT1 MB231_control_K27_UT
- GSM7989288 MB231_control_K27_UT2 MB231_control_K27_UT
- GSM7989289 MB231_control_K27_TW1 MB231_control_K27_TW
- GSM7989290 MB231_control_K27_TW2 MB231_control_K27_TW
- GSM7989291 MB231_Fn14KO_K27_UT1 MB231_Fn14KO_K27_UT
- GSM7989292 MB231_Fn14KO_K27_UT2 MB231_Fn14KO_K27_UT
- GSM7989293 MB231_Fn14KO_K27_TW1 MB231_Fn14KO_K27_TW
- GSM7989294 MB231_Fn14KO_K27_TW2 MB231_Fn14KO_K27_TW
- GSM7989295 Hs578T_control_K27_UT1 Hs578T_control_K27_UT
- GSM7989296 Hs578T_control_K27_UT2 Hs578T_control_K27_UT
- GSM7989297 Hs578T_control_K27_TW1 Hs578T_control_K27_TW
- GSM7989298 Hs578T_control_K27_TW2 Hs578T_control_K27_TW
- GSM7989299 Hs578T_Fn14KO_K27_UT1 Hs578T_Fn14KO_K27_UT
- GSM7989300 Hs578T_Fn14KO_K27_UT2 Hs578T_Fn14KO_K27_UT
- GSM7989301 Hs578T_Fn14KO_K27_TW1 Hs578T_Fn14KO_K27_TW
- GSM7989302 Hs578T_Fn14KO_K27_TW2 Hs578T_Fn14KO_K27_TW
- GSE251868 TWEAK/Fn14 signalling in Breast Cancer (HER2 H3K27ac ChIP-seq) 10 samples shares h3k27ac, tweak, fn14, chip-seq, breast
- GSE251867 TWEAK/Fn14 signalling in Breast Cancer (MAFG ChIP-seq) 16 samples shares tweak, fn14, chip-seq, breast
- GSE231479 TWEAK/Fn14 signalling in Breast Cancer [cell line K27 ChIP] 24 samples shares tweak, fn14, breast
- GSE231482 TWEAK/Fn14 signalling in Breast Cancer [patient K27 ChIP] 24 samples shares tweak, fn14, breast
- GSE231477 TWEAK/Fn14 signalling in Breast Cancer [cell line ATAC-seq] 14 samples shares tweak, fn14, breast
- GSE231481 TWEAK/Fn14 signalling in Breast Cancer [patient ATAC-seq] 12 samples shares tweak, fn14, breast
- GSE231483 TWEAK/Fn14 signalling in Breast Cancer 64 samples shares tweak, fn14, breast
- GSE231480 TWEAK/Fn14 signalling in Breast Cancer [cell line RNA-seq] 24 samples shares tweak, fn14, breast
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.