Quant-seq on COMPASS-degron cells

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UID: 10926

Author(s): Wang, Hua* * MSK affiliated

Description: Summary from GEO:

"Here, we showed that acute lost H3K4me3 induces rapid reduction in global transcription with progressively increase in magnitude over the time-course cooccurrence with lost all H3K4 methylations."

Overall design from GEO:

"To define the primary effects of rapid H3K4me3 removal on transcription, we measured the synthesis of newly transcribed RNAs using a Thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) with a 0, 2, 8 and 24 hour time-course in the degron cells. DPY30mAID, DPY30-mAID degron cell; DPY30mAID_Kdm5dKO, Kdm5a and Kdm5b double knock out based on DPY30-mAID degron cell; RBBP5FKBP, RBBP5-FKBP degron cell. For all trans-retinoic acid (RA, Sigma-Aldrich, R2625-50MG) treatment, cells were induced with 1 μM RA and without LIF for the indicated time."

Subject of Study

Subject(s)

Access via GEO

Accession #: GSE181708

Access via BioProject

Accession #: PRJNA753077

Access via SRA

Accession #: SRP331674
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, BioProject, and SRA databases provide open access to these files.
Associated Publications: Wang H, Fan Z, Shliaha P, Miele M, Hendrickson R, Jiang X, Helin K. H3K4me3 regulates RNA polymerase II promoter-proximal pause-release. Nature. 2023; 615(7951):339-348.
Equipment Used: Illumina NextSeq 550
Sequencing and array capabilities for transcriptome, targeted resequencing and genotype sequencing
Dataset Format(s): TSV, TAR
Dataset Size: 55.7 MB

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