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| Status |
Public on Feb 14, 2024 |
| Title |
37°C, rep2 |
| Sample type |
SRA |
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| Source name |
yeast
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: BY4741/2
genotype: CBP80-PPX-PrA, SNAPf-YRA1
treatment: Grown at 25°C followed by temperature shift to 37°C and culture for 2 hour
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| Growth protocol |
For 25 and 30°C samples, yeast cells were grown in YPD at each temperature until OD around 1. For 37°C sample, cells grown at 25°C with OD around 1 was diluted by equal volume of pre-warmed media and initially incubated in the 37°C water bath for 15 min. The cells were further cutured in 37°C shaker for totally 2 hours.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cell lysate was generated by cryo-grinding and RNA was extracted using RNA extraction kit (Zymo research, R2014).
3'tag seq library was prepared using QuantSeq (Lexogen) kit.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
2527_37deg_2
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| Data processing |
Unique sequence identifier (UMI) sequence was extracted and UMI, random primer seqence were trimed by UMI-tools (v1.0.1)
Adapter, poly A tail, low quality sequences at 3' end were trimed using bbduk (Bbmap v38.79)
Mapping of trimed reads on S. cerevisiae genome was performed by STAR (v2.7.10a)
PCR duplicates were removed by UMI-tools (v1.0.1)
Read count within the annotated genes was performed by htseq-counts (htseq v2.0.2)
Differentially expression analysis across the samples were performed using DESeq2 (v 1.38.2)
Assembly: GCF_000146045.2_R64
Supplementary files format and content: raw_readcounts_temp.xlsx file provides low read counts table. Each column has read count on every annotated genes in each samples.
Supplementary files format and content: Normalized_read_counts_temp.xlsx provides normalized read count generated by DESeq2. Each column has normalized read count on every annotated genes in each samples.
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| Submission date |
Mar 08, 2023 |
| Last update date |
Feb 14, 2024 |
| Contact name |
Ben Montpetit |
| E-mail(s) |
benmontpetit@ucdavis.edu
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| Organization name |
University of California, Davis
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| Department |
Viticulture and Enology
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| Street address |
One Shields Ave
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| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
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| Platform ID |
GPL19756 |
| Series (1) |
| GSE226974 |
Gene expression analysis of yeast grown at 25, 30 and 37°C |
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| Relations |
| BioSample |
SAMN33687463 |
| SRA |
SRX19604799 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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