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Tyrosine phosphorylation of CARM1 promotes its enzymatic activity and alters its target specificity

GSE200973 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 20 samples Submitted 2024/04/03 Platform GPL24676
At a glance

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)
Samples
20 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
Tyrosine phosphorylation of CARM1 promotes its enzymatic activity and alters its target specificityNature communications · 2024
Summary (written by the submitters)
CARM1 Y149F, Y334F or Y149F/Y334F mutants have decreased activtiy to dimethylate RUNX1.
Published in
Tyrosine phosphorylation of CARM1 promotes its enzymatic activity and alters its target specificity
Itonaga H, Mookhtiar AK, Greenblatt SM et al. · Nature communications 2024 · PMID 38649367 · doi:10.1038/s41467-024-47689-4
This dataset
Open GSE200973 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE200973_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA827788 and SRA study SRP370854. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38649367) ↗
Study design
8 conditions, mostly in duplicate
CARM1-WT_RUNX1R319me2a_ChIPSeq ×2 CARM1-Y149F_RUNX1R319me2a_ChIPSeq ×2 CARM1-Y334F_RUNX1R319me2a_ChIPSeq ×2 CARM1-Y149/Y334F_RUNX1R319me2a_ChIPSeq ×2 CARM1-WT_RUNX1_ChIPSeq ×2 CARM1-Y149F_RUNX1_ChIPSeq ×2 CARM1-Y334F_RUNX1_ChIPSeq ×2 CARM1-Y149/Y334F_RUNX1_ChIPSeq ×2 +4 more

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 20 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.

Samples in this study
Datasets on a similar topic

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