GEO series
The BOD1L subunit of the SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylation [single_end_RNAseq]
At a glance
DNA methylation · mouse · 36 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Mus musculus (mouse)
- Samples
- 36 samples: 17 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.
Summary (written by the submitters)
Background SETD1A is the histone 3 lysine 4 (H3K4) methyltransferase central to the mammalian version of the highly conserved eight subunit Set1 complex (Set1C) that apparently conveys H3K4 trimethylation (H3K4me3) onto all active Pol II promoters. Accordingly, the Setd1a mouse knock-out dies in early embryogenesis at the epiblast stage and mouse embryonic stem cells (ESCs) die when SETD1A is removed.
Read the full summary ↓
Results We report that ESC death is accompanied by loss of expression of DNA repair genes and accumulating DNA damage. BOD1L and BOD1 are homologs of the yeast Set1C subunit, Shg1, and subunits of the mammalian SETD1A and B complexes. We show that the Shg1 homology region binds to a highly conserved central a-helix in SETD1A and B. Like mutagenesis of Shg1 in yeast, conditional mutagenesis of Bod1l in ESCs promoted increased H3K4 di- and tri-methylation but also, like loss of SETD1A, loss of expression of DNA repair genes, increased DNA damage and cell death. Conclusions In contrast to similar losses of DNA repair gene expression, the converse changes in H3K4 methylation after loss of SETD1A or BOD1L implies that H3K4 methylation is not essential for expression of the DNA repair network genes. Because BOD1L becomes highly phosphorylated after DNA damage and acts to protect damaged replication forks, the SETD1A complex, and BOD1L in particular, are key nodes for the DNA damage repair network.
This dataset
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.
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 GSE319677_RAW.tar (it can run to tens of gigabytes).
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.
What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA1424948 and SRA study SRP677724. Searching any of these in the dataset finder brings you back here.
Study design
17 conditions, mostly in duplicate
ESC2i Bod1L KO Tamoxifen biol ×2
ESC2i Bod1L WT biol ×2
ESC2i Mll2 KO Tamoxifen biol ×2
ESC2i Mll2 WT biol ×2
ESC2i Setd1a KO Tamoxifen biol ×2
ESC2i Setd1a WT biol ×2
ESCFCS Bod1L KO Tamoxifen biol ×2
ESCFCS Bod1L WT biol ×2
+11 more
Supports a between-group comparison across 34 samples.
How we read this: 17 replicated groups read from 36 sample titles; they account for 34 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
- GSM9523457 ESC2i Bod1L KO Tamoxifen biol rep 1 ESC2i Bod1L KO Tamoxife…
- GSM9523458 ESC2i Bod1L WT biol rep 1 ESC2i Bod1L WT biol
- GSM9523459 ESC2i Bod1L KO Tamoxifen biol rep 2 ESC2i Bod1L KO Tamoxife…
- GSM9523460 ESC2i Bod1L WT biol rep 2 ESC2i Bod1L WT biol
- GSM9523461 ESC2i Mll2 KO Tamoxifen biol rep 1 ESC2i Mll2 KO Tamoxifen…
- GSM9523462 ESC2i Mll2 WT biol rep 1 ESC2i Mll2 WT biol
- GSM9523463 ESC2i Mll2 KO Tamoxifen biol rep 2 ESC2i Mll2 KO Tamoxifen…
- GSM9523464 ESC2i Mll2 WT biol rep 2 ESC2i Mll2 WT biol
- GSM9523465 ESC2i Setd1a KO Tamoxifen biol rep 1 ESC2i Setd1a KO Tamoxif…
- GSM9523466 ESC2i Setd1a WT biol rep 1 ESC2i Setd1a WT biol
- GSM9523467 ESC2i Setd1a KO Tamoxifen biol rep 2 ESC2i Setd1a KO Tamoxif…
- GSM9523468 ESC2i Setd1a WT biol rep 2 ESC2i Setd1a WT biol
- GSM9523469 ESCFCS Bod1L KO Tamoxifen biol rep 1 ESCFCS Bod1L KO Tamoxif…
- GSM9523470 ESCFCS Bod1L WT biol rep 1 ESCFCS Bod1L WT biol
- GSM9523471 ESCFCS Bod1L KO Tamoxifen biol rep 2 ESCFCS Bod1L KO Tamoxif…
- GSM9523472 ESCFCS Bod1L WT biol rep 2 ESCFCS Bod1L WT biol
- GSM9523473 ESCFCS Mll2 KO Tamoxifen biol rep 1
- GSM9523474 ESCFCS Mll2 WT biol rep 1 ESCFCS Mll2 WT biol
- GSM9523475 ESCFCS Mll2 KO Tamoxifen biol rep 2
- GSM9523476 ESCFCS Mll2 WT biol rep 2 ESCFCS Mll2 WT biol
- GSM9523477 ESCFCS Setd1a KO Tamoxifen biol rep 1 ESCFCS Setd1a KO Tamoxi…
- GSM9523478 ESCFCS Setd1a WT biol rep 1 ESCFCS Setd1a WT biol
- GSM9523479 ESCFCS Setd1a KO Tamoxifen biol rep 2 ESCFCS Setd1a KO Tamoxi…
- GSM9523480 ESCFCS Setd1a WT biol rep 2 ESCFCS Setd1a WT biol
- GSM9523481 EpiSC Bod1L KO Tamoxifen biol rep 1 EpiSC Bod1L KO Tamoxife…
- GSM9523482 EpiSC Bod1L WT biol rep 1 EpiSC Bod1L WT biol
- GSM9523483 EpiSC Bod1L KO Tamoxifen biol rep 2 EpiSC Bod1L KO Tamoxife…
- GSM9523484 EpiSC Bod1L WT biol rep 2 EpiSC Bod1L WT biol
- GSM9523485 EpiSC Mll2 KO Tamoxifen biol rep 1 EpiSC Mll2 KO Tamoxifen…
- GSM9523486 EpiSC Mll2 WT biol rep 1 EpiSC Mll2 WT biol
- GSM9523487 EpiSC Mll2 KO Tamoxifen biol rep 2 EpiSC Mll2 KO Tamoxifen…
- GSM9523488 EpiSC Mll2 WT biol rep 2 EpiSC Mll2 WT biol
- GSM9523489 EpiSC Setd1a KO Tamoxifen biol rep 1 EpiSC Setd1a KO Tamoxif…
- GSM9523490 EpiSC Setd1a WT biol rep 1 EpiSC Setd1a WT biol
- GSM9523491 EpiSC Setd1a KO Tamoxifen biol rep 2 EpiSC Setd1a KO Tamoxif…
- GSM9523492 EpiSC Setd1a WT biol rep 2 EpiSC Setd1a WT biol
Datasets on a similar topic
- GSE319676 The BOD1L subunit of the SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylation [paired_end_RNAseq] 12 samples shares setd1a, bod1l, h3k4, trimethylation, restraining, sustains, subunit, complex
- GSE165460 Induction of senescence upon loss of the Ash2l subunit of histone H3K4 methyltransferase complexes (ChIP-Seq) 20 samples shares h3k4, subunit, complex
- GSE208365 Identify H3K4Me3 occupancy on genome in Setd1a Knock out (KO) mouse undifferentiated pleomorphic sarcoma cells 10 samples shares setd1a, h3k4
- GSE7815 Histone H3K4 and H3K27 trimethylation analysis in ES cells, Mefs and induced pluriptent cells. 26 samples shares h3k4, trimethylation
- GSE250276 Epigenetic maintenance of neural stem cell quiescence in the adult mouse hippocampus via Setd1a [RNA-Seq] 48 samples shares setd1a
- GSE229238 DNA methylation constrains nucleosome retention in sperm and H3K4 methylation deposition in early mouse embryos [RNA-seq 2] 42 samples shares h3k4
- GSE335970 KMT2C catalytic activity regulates enhancer H3K4me1 and synaptic gene expression in cortical excitatory neurons [RNA-Seq] 39 samples shares h3k4
- GSE309712 Broad H3K4me3 domains support oocyte genome silencing and maturation but are dispensable for repression in early embryos 35 samples shares h3k4
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