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| Status |
Public on Jul 08, 2022 |
| Title |
ime4_2H_R3 |
| Sample type |
SRA |
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| Source name |
SK1 pCUP-IME1
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell line: SK1 pCUP-IME1
cell type: diploid meiotic yeast
genotype: ime4 mutant
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| Growth protocol |
Synchronous meiotic entry was performed in standard procedure as described (Schwartz et al., 2013). Briefly, respiratory proficient diploids were pre-selected on 1% yeast extract, 2% peptone, 3% glycerol, 2% agar for 24 hr at 30°C, transferred for another 24 hr of growth in 1% yeast extract, 2% peptone, 4% dextrose at 30°C and 170 rpm, diluted in BYTA media (1% yeast extract, 2% tryptone, 1% potassium acetate, 50 nM potassium phthalate) to OD600 = 0.2 and incubated for another 16 hr incubation at 30°C and 170 rpm. Next, cells were washed once with sterile milliQ water and resuspended in SPO medium (0.3% potassium acetate) at OD600 = 2.0 and incubated at 30°C and 170 rpm. To induce IME1 in the pCUP-IME1 background, 50 μM of copper (II) Sulfate was added after 2 hr in SPO. Cells were isolated from SPO at the indicated time points by centrifugation (3 min at 8,000 g).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted on 2.0 - 3.0 OD of 2 OD/ml yeast cells using a standard hot acid phenol protocol.
mRNA-seq libraries were generated from 500 ng of total RNA using TruSeq® Stranded mRNA Library Prep kit and TruSeq® RNA Single Indexes kits A and B (Illumina, Cat#20020595) according to manufacturer's instructions. Quantity and quality of the started material and final librairies were checked using a Qubit™ fluorometer (Invitrogen™) and Agilent Bioanalyzer. Resulting libraries were sequenced in 50-length Single-Read on a HiSeq 4000 machine (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
50 nt read length
Table S1
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| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were mapped onto the SK1 assembly of the Saccharomyces cerevisiae genome (SK1 MvO V1; SK1_SGD_2018_NCSL00000000) using Tophat 2.0.14 (Kim et al., 2013; Trapnell et al., 2009) and bowtie version 2-2.1.0 (Langmead et al., 2009). Only uniquely mapped reads have been retained for further analyses.
Quantification of gene expression has been performed with HTSeq-0.6.1 (Anders et al., 2015), using intersection-nonempty mode, and annotations coming from the Saccharomyces Genome Database (SGD). Only non-ambiguously assigned reads have been retained for further analyses.
Comparisons of interest have been performed using R 3.5.1 with DEseq2 version 1.22.1 (Love et al., 2014). More precisely, read counts were normalized from the estimated size factors using the median-of-ratios method (Anders and Huber, 2010) and a Wald test was used to estimate the p-values. P-values were then adjusted for multiple testing with the Benjamini and Hochberg method (Benjamini and Hochberg, 1995).
Assembly: SK1 MvO V1: SK1_SGD_2018_NCSL00000000
Supplementary files format and content: Table S1. Excel file for mRNA-seq data include for each detectable transcript: raw read count, normalized values, gene informations, log2foldchange expression value in mutants vs WT, p-value and adjusted p-value
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| Submission date |
Apr 04, 2022 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Jérémy Scutenaire |
| E-mail(s) |
jeremy-scut@hotmail.fr
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| Organization name |
IGBMC
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| Street address |
1 rue Laurent Fries
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| City |
Illkirch |
| ZIP/Postal code |
67400 |
| Country |
France |
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| Platform ID |
GPL21656 |
| Series (2) |
| GSE200087 |
The S. cerevisiae m6A reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts [RNA-seq] |
| GSE200089 |
The S. cerevisiae m6A reader Pho92 promotes timely meiotic recombination by controlling key methylated transcripts. |
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| Relations |
| BioSample |
SAMN27282260 |
| SRA |
SRX14720661 |
| 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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