Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 6
Release date: Jul 3 2018
Last update date: Oct 2 2018
Access: Public
Dataset link Casein Kinase 2 Mediated Phosphorylation of Spt6 Modulates Histone dynamics and Regulates Spurious Transcription (RNA-Seq)

Experimental Protocol


Cells from CK2ts and spt6-7SA mutant strains and a WT strain were grown in YPD to an OD600 of 0.5 at 30°C and shifted to 39°C for 2h before RNA extraction. Total RNA was extracted using the hot-phenol method. Prior to library preparation, total RNA was depleted for ribosomal RNA using the Ribo-zero Gold yeast kit (Epicentre-Illumina). RNA-seq experiments were performed following TruSeq stranded total RNA illumina protocol and Illumina next generation sequencing was performed as 50 base pairs single-end reads on an Illumina Hi-Seq2000 (McGill University and Génome Québec Innovation Centre, Montréal, Canada). The sequenced reads from each sample were preprocessed with Trimmomatic (Bolger et al., 2014) and aligned with bwa (Li et al., 2009) to S.cerevisiae genome assembly R64-1-1 (GCA_000146045.2) and the numbers of reads for each exon annotated in Ensembl Release 77 was calculated for both the sense and antisense strands using SAMtools.

Repositories


GEO

GSE108482

ENA

SRP127487

BioProject

PRJNA427393

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Contact


Amine Nourani