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Sample GSM4832627

Query DataSets for GSM4832627

Status

Public on Oct 20, 2020

Title

SD0hr2_S8: w303 Spores incubated for 0 hour in SC with 0.002% glucose, replicate no.2

Sample type

SRA

Source name

w303 Spores

Organism

Saccharomyces cerevisiae W303

Characteristics

strain: w303
genotype: MATa; his3-11_15; leu2-3_112; ura3-1; trp1 D2; ade2-1; can1-100
tissue: spores

Treatment protocol

To isolate the un-germinated spores, we treated the 1-mL samples with zymolyase (786-036, G-Biosciences). Zymolyase lysed vegetative cells that formed from germinated spores, thus ensuring that we only collected RNA from un-germinated spores for sequencing.

Growth protocol

We collected un-germinated spores by first collecting 1 ml samples of spores that were incubated in a 0.002%-glucose at 0, 16, 48, and 96 hours after the incubation began.

Extracted molecule

total RNA

Extraction protocol

We then extracted the RNA from the leftover, un-germinated spores RiboPure Yeast Kit (Ambion, Life Technologies) as described by its protocol. Next, we prepared the cDNA library with the 3' mRNA-Seq library preparation kit (Quant-Seq, Lexogen) as described by its protocol.
Next, we prepared the cDNA library with the 3' mRNA-Seq library preparation kit (Quant-Seq, Lexogen) as described by its protocol. Afterwards, we loaded the cDNA library on an Illumina MiSeq with the MiSeq Reagent Kit c2 (Illumina) as described by its protocol.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina MiSeq

Data processing

We analyzed the resulting RNA-Seq data (.fastq files) as previously described (Trapnell et al., Nat Protoc 2012).
We removed the adapter contamination, polyA read through, and low quality tails for each sample by using BBDuk (JGI, version 36.85) with following settings: k=13, ktrim=r, forcetrimleft=11, useshortkmers=t, mink=5, qtrim=t, trimq=10, minlength=20.
We performed read aligment using TopHat (version 2.1.1) with Bowtie (version 2.2.9.0).
We performed read assembly and analysis of differential gene expression data using Cufflinks (version 2.2.1).
We optionally used R package called CummeRbund (version 2.7.2) from Bioconductor (version 3.11) to analyze and visualize RNA-seq data. We used the transcriptional modules listed in “transcriptional_modules_list.txt” for grouping the relevant genes into transcriptional modules.
Genome_build: Saccharomyces cerevisiae, Ensembl R64-1-1
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values per condition per gene.

Submission date

Oct 19, 2020

Last update date

Oct 20, 2020

Contact name

Theo Maire

E-mail(s)

theo.maire01@gmail.com

Organization name

Delft University of Technology

Department

Bionanoscience