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SRX23677963: GSM8086667: Scer, optimal growth, RNA, rep1; Saccharomyces cerevisiae; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 27.1M spots, 2.7G bases, 877.5Mb downloads

External Id: GSM8086667_r1
Submitted by: National Research Collections Australia, CSIRO
Study: Effects of formalin-fixation on FAIRE-Seq and MNase-Seq signatures in yeast (RNA-Seq)
show Abstracthide Abstract
Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we first sought to understand the effect of prolonged formalin fixation on the read alignment signatures resulting from FAIRE and MNase treatment. Here we cultured yeast (Saccharomyces cerevisiae) under normal and heat-shock conditions then fixed the cells with formalin for 15 minutes, 1 hour, 6 hours, and 24 hours. We found that heavy formalin fixation modulates rather than eliminates signatures of differential chromatin accessibility and enables semi-quantitative estimates of relative gene expression in this yeast model. Overall design: FAIRE and MNase treatment of Saccharomyces cerevisiae?(strain?BJ5464 auxotroph??URA3) in a formalin-fixation time series
Sample: Scer, optimal growth, RNA, rep1
SAMN40008068 • SRS20508685 • All experiments • All runs
Library:
Name: GSM8086667
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: We resuspended three 2 mL aliquots per culture in 450 mL RLT Buffer and followed the manufacturer's instructions for the Qiagen RNeasy plant mini kit, eluting in 30 mL nuclease-free water. Illumina stranded mRNA library prep
Runs: 1 run, 27.1M spots, 2.7G bases, 877.5Mb
Run# of Spots# of BasesSizePublished
SRR2802615227,121,0052.7G877.5Mb2024-03-01

ID:
31961380

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