Investigation of melanoma cell chromatin acetylation states with high and low levels of ALDH1A3
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 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
- MelanomaThis series is part of our curated briefing on it.
- Samples
- 20 samples: 10 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
- ALDH1A3-acetaldehyde metabolism potentiates transcriptional heterogeneity in melanomaCell reports · 2024
Read the full summary ↓
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 GSE243834_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 PRJNA1020130 and SRA study SRP462682. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 10 replicated groups read from 20 sample titles; they account for 20 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.
- GSM7796286 A375_Ctrl_H3Ac_ChIP_rep1 A375_Ctrl_H3Ac_ChIP
- GSM7796287 A375_Ctrl_H3Ac_ChIP_rep2 A375_Ctrl_H3Ac_ChIP
- GSM7796288 A375_ALDH1A3KO_H3Ac_ChIP_rep1 A375_ALDH1A3KO_H3Ac_ChIP
- GSM7796289 A375_ALDH1A3KO_H3Ac_ChIP_rep2 A375_ALDH1A3KO_H3Ac_ChIP
- GSM7796290 A375_Ctrl_input_rep1 A375_Ctrl_input
- GSM7796291 A375_Ctrl_input_rep2 A375_Ctrl_input
- GSM7796292 A375_ALDH1A3KO_input_rep1 A375_ALDH1A3KO_input
- GSM7796293 A375_ALDH1A3KO_input_rep2 A375_ALDH1A3KO_input
- GSM8262208 H3K23ac_Ctrl_R1 H3K23ac_Ctrl
- GSM8262209 H3K23ac_Ctrl_R2 H3K23ac_Ctrl
- GSM8262210 H3K23ac_KD_R1 H3K23ac_KD
- GSM8262211 H3K23ac_KD_R2 H3K23ac_KD
- GSM8262212 H3K27ac_Ctrl_R1 H3K27ac_Ctrl
- GSM8262213 H3K27ac_Ctrl_R2 H3K27ac_Ctrl
- GSM8262214 H3K27ac_KD_R1 H3K27ac_KD
- GSM8262215 H3K27ac_KD_R2 H3K27ac_KD
- GSM8262216 IgG_Ctrl_R1 IgG_Ctrl
- GSM8262217 IgG_Ctrl_R2 IgG_Ctrl
- GSM8262218 IgG_KD_R1 IgG_KD
- GSM8262219 IgG_KD_R2 IgG_KD
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- GSE230489 RNA-sequencing of cutaneous melanoma and non-small cell lung cancer biopsies 38 samples same disease briefing · shares melanoma
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- GSE123728 Clinical and Immunologic Activity of a Single Dose of Neoadjuvant PD-1 Blockade and Predictors of Clinical Outcomes in Resectable Melanoma 24 samples same disease briefing · shares melanoma
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.