Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma
DNA methylation · mouse · 21 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Mus musculus (mouse)
- Samples
- 21 samples: 18 distinct titles, 3 of them repeatedGroups 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.
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 GSE269463_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 PRJNA1122072 and SRA study SRP512853. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 21 sample titles: 18 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.
- GSM8311154 SMB21_DMSO_A
- GSM8311155 SMB21_DMSO_B
- GSM8311156 SMB21_DMSO_C
- GSM8311157 SMB21_AZA_A
- GSM8311158 SMB21_AZA_B
- GSM8311159 SMB21_AZA_C
- GSM8311160 SMB55_DMSO_A
- GSM8311161 SMB55_DMSO_B
- GSM8311162 SMB55_DMSO_C
- GSM8311163 SMB55_AZA_A
- GSM8311164 SMB55_AZA_B
- GSM8311165 SMB55_AZA_C
- GSM8316087 SMB21_DMSO_A
- GSM8316088 SMB21_DMSO_B
- GSM8316089 SMB21_DMSO_C
- GSM8316090 SMB21_AZA_2h_A
- GSM8316091 SMB21_AZA_2h_B
- GSM8316092 SMB21_AZA_2h_C
- GSM8316093 SMB21_AZA_24h_A
- GSM8316094 SMB21_AZA_24h_B
- GSM8316095 SMB21_AZA_24h_C
- GSE260851 Genetic modeling of ELP1-associated Sonic hedgehog medulloblastoma identifies MDM2 as a selective therapeutic target 161 samples shares medulloblastoma, hedgehog
- GSE324386 Transcriptomic profiling of CRISPR-Cas9 knockout of RAD51D, LIMCH1, and BRD9 in MC38 colorectal cancer cells reveals regulation of PD-L1 expression 29 samples shares crispr-cas9, knockout
- GSE260659 Genetic modeling of ELP1-associated Sonic hedgehog medulloblastoma identifies MDM2 as a selective therapeutic target 24 samples shares medulloblastoma, hedgehog
- GSE263249 Genome-wide distribution of H3K9me3, RNA polymerase II, Rloop, DDX55 and HA-tagged DDX55 in WT and DDX55 knockout CD4 naive T cells 23 samples shares genome-wide, knockout
- GSE291945 The Hira complex regulates Gli3R-dependent transcription in Hedgehog signaling and medulloblastoma cell growth and migration 10 samples shares medulloblastoma, hedgehog
- GSE27713 Genome-wide analysis of gene expression patterns in mir-122 knockout mice livers 7 samples shares genome-wide, knockout
- GSE267053 Rescuing DNMT1 Fails to Fully Reverse the Molecular and Functional Repercussions of Its Loss in Mouse Embryonic Stem Cells. 96 samples shares dnmt1
- GSE180529 A Dominant mutation in Dnmt1 leads epigenetic changes (Bulk RNAseq) 92 samples shares dnmt1
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.