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BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A (RNA-seq)

GSE258789 Homo sapiens (human) RNA-seq (gene expression) 20 samples Submitted 2024/06/25 Platform GPL18573Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 20 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
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
BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1ANucleic acids research · 2024
Summary (written by the submitters)
The H3K4 methyltransferase SETD1A plays an essential role in both development and cancer. However, essential components involved in SETD1A chromatin binding remain unclear. Here, we discovered that BOD1L exhibits the highest correlated co-dependency with SETD1A in human cancer cell lines. BOD1L knockout reduces leukemia cells in vitro and in vivo, and mimics the transcriptional profiles observed in SETD1A knockout cells.
Read the full summary ↓
The loss of BOD1L immediately reduced SETD1A distribution at transcriptional start sites (TSS) and induces transcriptional elongation defect along with the increasing of RNA polymerase II at TSS, but did not cause the reduction of H3K4me3. The Shg1 domain of BOD1L has a DNA binding ability, and recruit SETD1A to chromatin through the association with SETD1A FLOS domain. In addition, the BOD1L-SETD1A complex associates with transcriptional regulators, including E2Fs. These results reveal that BOD1L mediates chromatin and SETD1A, and regulates the non-canonical function of SETD1A in transcription.
Published in
BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A
Hoshii T, Kikuchi S, Kujirai T et al. · Nucleic acids research 2024 · PMID 38989615 · doi:10.1093/nar/gkae605
This dataset
Open GSE258789 in finder → Find more human RNA-seq 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 GSE258789_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1080267 and SRA study SRP491647. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38989615) ↗
Study design
8 conditions, mostly in duplicate
MOLM13_sgAAVS_2_Dox_4d ×4 MOLM13_sgCCR5_255_Dox_4d ×4 MOLM13_sgBOD1L_243_Dox_4d ×2 MOLM13_sgBOD1L_437_Dox_4d ×2 MOLM13_sgRBBP5_1_Dox_4d ×2 MOLM13_sgRBBP5_2_Dox_4d ×2 MOLM13_FKBP-BOD1L_DMSO_24h ×2 MOLM13_FKBP-BOD1L_dTAG13_24h ×2

Supports a between-group comparison across 20 samples.

How we read this: 8 replicated groups read from 20 sample titles; they account for 20 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
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