Systemic comparison of dCas9-based DNA methylation editing systems for specificity and stability [RNAseq_firstRun]
DNA methylation · human · 17 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Samples
- 17 samples: 17 samples, each with a distinct title — no replicated groupsGroups 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
- Comprehensive profiling of CRISPR/dCas9 epigenome editors indicates a complex link between on and off target effectsGenome biology · 2026
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 GSE297430_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 beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA1263832 and SRA study SRP586000. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 17 sample titles: 17 distinct titles with little repetition. 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.
- GSM8991234 3A3A_BACH2_g8_3d (RNA-Seq)
- GSM8991235 3A3L_BACH2_g8_3d (RNA-Seq)
- GSM8991236 3A_KRAB_BACH2_g8_3d (RNA-Seq)
- GSM8991237 MSssI_BACH2_g8_3d (RNA-Seq)
- GSM8991238 SunTag_BACH2_g8_3d (RNA-Seq)
- GSM8991239 3A_BACH2_g8_3d (RNA-Seq)
- GSM8991240 mut3A_BACH2_g8_3d (RNA-Seq)
- GSM8991241 CRISPRoff_BACH2_g8_3d (RNA-Seq)
- GSM8991242 dDNMT3A_BACH2_g8_3d (RNA-Seq)
- GSM8991243 3A3A_NTC_3d (RNA-Seq)
- GSM8991244 3A3L_NTC_3d (RNA-Seq)
- GSM8991245 3A_KRAB_NTC_3d (RNA-Seq)
- GSM8991246 MSssI_NTC_3d (RNA-Seq)
- GSM8991247 SunTag_NTC_3d (RNA-Seq)
- GSM8991248 3A_NTC_3d (RNA-Seq)
- GSM8991249 mut3A_NTC_3d (RNA-Seq)
- GSM8991250 CRISPRoff_NTC_3d (RNA-Seq)
- GSE284289 Removal of promoter DNA methylation by epigenome editing reverses HBG silencing [RNA-seq] 40 samples shares methylation, editing
- GSE336584 Neocentromeres fail to maintain DNA methylation boundaries, driving CENP-A drift, instability, and chromosome missegregation 60 samples shares methylation, stability
- GSE271704 5G-exposed human skin cells do not respond with altered gene expression and methylation profiles [RNA-Seq] 120 samples shares methylation
- GSE328878 Transcriptomic comparison of RA vs healthy monocytes undergoing different ex vivo activation conditions 72 samples shares comparison
- GSE297676 Comparison of axicabtagene ciloleucel and tisagenlecleucel patient CAR-T cell products by single cell RNA sequencing 57 samples shares comparison
- GSE161245 Comparison of bronchial epithelial cells obtained by bronchoscopy from mild asthma patients, moderate asthma patients, severe asthma patients and healthy controls 55 samples shares comparison
- GSE281750 The bladder cancer m6A landscape is defined by global methylation dilution and focal 3′-UTR hypermethylation 54 samples shares methylation
- GSE293032 Transcriptomic comparison of hepatocytes derived from a panel of human induced pluripotent stem cells with different ethnicities 54 samples shares comparison
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.