MyoD is Essential in Rhabdomyosarcoma by Promoting Survival Through Differentiation and CYLD
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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
- Soft tissue sarcomaThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × RH30, sgRNA scramble, vs 3 × RH30, sgRNA targeting MyoD, vs 3 × RH30 SR, vs 3 × RH30 IkBa-SR;MyoD CRISPR clone 29,Groups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed expression table (series matrix) and the array files, from NCBI.
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 GSE224179_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 PRJNA930019 and SRA study SRP420315. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM7016932 RH30, sgRNA scramble, biological rep1 RH30, sgRNA scramble,
- GSM7016933 RH30, sgRNA scramble, biological rep2 RH30, sgRNA scramble,
- GSM7016934 RH30, sgRNA scramble, biological rep3 RH30, sgRNA scramble,
- GSM7016935 RH30, sgRNA targeting MyoD, biological rep1 RH30, sgRNA targeting M…
- GSM7016936 RH30, sgRNA targeting MyoD, biological rep2 RH30, sgRNA targeting M…
- GSM7016937 RH30, sgRNA targeting MyoD, biological rep3 RH30, sgRNA targeting M…
- GSM7016938 RH30 SR, replicate 1 RH30 SR,
- GSM7016939 RH30 SR, replicate 2 RH30 SR,
- GSM7016940 RH30 SR, replicate 3 RH30 SR,
- GSM7016941 RH30 IkBa-SR;MyoD CRISPR clone 29, replicate 1 RH30 IkBa-SR;MyoD CRISP…
- GSM7016942 RH30 IkBa-SR;MyoD CRISPR clone 29, replicate 2 RH30 IkBa-SR;MyoD CRISP…
- GSM7016943 RH30 IkBa-SR;MyoD CRISPR clone 29, replicate 3 RH30 IkBa-SR;MyoD CRISP…
- GSE274640 MYOD1L122R induces cancer stem cell pathways to impart chemotherapy and radiation-resistance in aggressive rhabdomyosarcoma. 80 samples same disease briefing · shares rhabdomyosarcoma, myod
- GSE279337 Dependence of PAX3-FOXO1 chromatin occupancy on ETS1 at important disease-promoting genes exposes new targetable vulnerability in Fusion-Positive Rhabdomyosarcoma 40 samples same disease briefing · shares rhabdomyosarcoma, promoting
- GSE288065 Transcriptional Heterogeneity of Progression in MYOD1-mutant spindle cell rhabdomyosarcoma 7 samples same disease briefing · shares rhabdomyosarcoma, myod
- GSE224170 Chromatin status of rhabdomyosarcoma (RMS) cell line RH30 in repsonse to MyoD CRISPR/Cas9 deletion [RMS ATAC-seq] 6 samples same disease briefing · shares rhabdomyosarcoma, myod
- GSE312030 Combined inhibition of HRAS and MEK induces tumor regression and restores myogenic differentiation in HRAS-mutant rhabdomyosarcoma 159 samples same disease briefing · shares rhabdomyosarcoma
- GSE303028 CDK8 Inhibition Releases the Muscle Differentiation Blockade in Fusion-driven Alveolar Rhabdomyosarcoma 104 samples same disease briefing · shares rhabdomyosarcoma
- GSE303151 CDK8 Inhibition Releases the Muscle Differentiation Blockade in Fusion-driven Alveolar Rhabdomyosarcoma [CUT&RUN] 50 samples same disease briefing · shares rhabdomyosarcoma
- GSE300974 CDK8 Inhibition Releases the Muscle Differentiation Blockade in Fusion-driven Alveolar Rhabdomyosarcoma [RNA-seq] 30 samples same disease briefing · shares rhabdomyosarcoma
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.