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SRX22544822: GSM7904042: hmo1△ yeast, replicate 1; Saccharomyces cerevisiae; OTHER
1 ILLUMINA (NextSeq 500) run: 17.5M spots, 1.3G bases, 634.3Mb downloads

External Id: GSM7904042_r1
Submitted by: University of Alabama at Birmingham
Study: Investigating the role of Hmo1 in transcription by Pol I in yeast.
show Abstracthide Abstract
The purpose of this study was to investigate the role of the yeast protein, high mobility group protein (Hmo1), in rRNA synthesis. For over twenty years, Hmo1 has been proposed to be an activator of transcription by Pol I, but its regulatory mechanism remains largely undefined. Therefore, we used native elongating transcript sequencing (NET-seq) to explore the role of this factor in transcription by Pol I. Our NET-seq results demonstrated that in cells lacking Hmo1 (hmo1D), Pol I occupancy was significantly increased across the rDNA template, indicating an increased pause propensity in these cells. These data suggest that Hmo1 is an important transcription elongation factor for Pol I. Overall design: Triplicate NET-seq libraries were generated for wild-type (WT) and hmo1? yeast strains. Please note that the WT samples (in GSE216460/PRJNA893665) were re-analysed in the current study: GEO accession title SRA accessions Biosample accession ========= ==== ========== ============= GSM6674347 WT yeast, untreated, rep1 SRR22028427/SRX18009711 SAMN31430711 GSM6674348 WT yeast, untreated, rep2 SRR22028426/SRX18009712 SAMN31430710 GSM6674349 WT yeast, untreated, rep3 SRR22028425/SRX18009713 SAMN31430709
Sample: hmo1△ yeast, replicate 1
SAMN38282512 • SRS19554205 • All experiments • All runs
Library:
Name: GSM7904042
Instrument: NextSeq 500
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: SINGLE
Construction protocol: Extraction methods was exactly the same as described in previously publications from our lab (data available at GSE142457, GSE166983, and GSE175553). In brief, cells were rapidly harvested and lysed under cryogenic conditions. An immunoprecipitation was performed to isolate Pol I and then an acidic phenol/chloroform extraction was used to extract total RNA. The generation of NET-seq libraries was performed exactly as previously published. In brief, a DNA linker containing a UMI sequence was ligated onto the 3' end of RNA reads. After ligation, a reverse transcription was performed, and DNA was circularized. Circular DNAs were amplified, libraries were purified with PCRClean DX beads, and reads were sequenced.
Runs: 1 run, 17.5M spots, 1.3G bases, 634.3Mb
Run# of Spots# of BasesSizePublished
SRR2684933817,454,9991.3G634.3Mb2023-11-20

ID:
30540157

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