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Sample GSM3362087

Query DataSets for GSM3362087

Status

Public on Aug 29, 2020

Title

spar sfp1 ko_B_30

Sample type

SRA

Source name

Yeast culture (BMW) - lag phase

Organism

Saccharomyces paradoxus

Characteristics

genotype: delta sfp1
replicate: B
growth phase: lag_30mins

Treatment protocol

Growth protocol

For log phase samples, cells were collected between O.D 0.6-0.8 Lag phase samples were collected at 30 mns and 60 mins post glucose repletion.

Extracted molecule

polyA RNA

Extraction protocol

RNA extraction Total RNA was isolated using the RNeasyMidi or Mini Kit (Qiagen) and instructions were followed for mechanical lysis.
Library construction was completed as previously described (Engreitz et al., 2013; Schwartz et al., 2013).
Rna-seq libraries were pooled and Paired-end 25 base pair reads were performed on Illumina’s Hiseq2000.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

Spar.OG.logFC.txt.gz
Spar.Gene.logFC.txt.gz
RNA-seq for delta sfp1 Saccharomyces paradoxus in Yeast culture (BMW) - lag phase (lag_30mins), replicateB. Used to generate column Spar_t30 in Spar.Gene.logFC.txt.gz
Other columns derived from microarrays (microarray submission in-process).

Data processing

Reads were mapped using RSEM (Li and Dewey, 2011) (version 1.2.11) utilizing Bowtie (Langmead, 2010) (version 1)
RSEM counts for the duplicated chromosome 2 in S. cerevisiae and S. paradoxus were similarly corrected by dividing the counts for genes on chromosome 2 by the median log fold change difference between genes on chromosome 2 and other genes between the WT and SFP1D mutant strains
We then used the edgeR package for R (Robinson, McCarthy and Smyth, 2010; McCarthy, Chen and Smyth, 2012) to TMM normalize the data and calculate the log fold changes and p-values of the gene expression differences between WT and SFP1D mutant strains.
Genome_build: The assembly (including transcriptome annotation information) from Scannell, et al. (Scannell et al., 2011) was used for S. paradoxus, and the r64 release of the S288C genome from the Saccharomyces Genome Database (Cherry et al., 2012) for S. cerevisiae. For C. glabrata, N. castellii, and K. lactis the genome and assembly and annotations were obtained from YGOB (v7 Aug 2012) and the S. pombe ASM294v2 genome assembly information was obtained from ENSEMBL (Vilella et al., 2009).
Supplementary_files_format_and_content: Files named "*.Gene.logFC.txt.gz" contain the gene-level (i.e. that species' genes) log-fold change (relative to WT) expression values for each species. Files names "*.OG.logFC.txt.gz" contain orthogroup-level logFC values for each species. orthology_melted_aliases.txt.gz contains the orthogroup mappings for each species. Note that because gene expression was measured using both microarrays and RNA-seq, this processed data includes the data from both. The gene expression microarrays that are part of this study and described in their own GEO entry (TBD). OG_to_Scer-GNs.txt.gz contains the orthogroup to S. cerevisiae systematic name mappings. Also included are raw counts (from RSEM) in files ending in ".counts.txt.gz" and copy-number-normalized TMM-normalized CPM values in files ending in ".TMM.txt.gz".

Submission date

Aug 30, 2018

Last update date

Aug 29, 2020

Contact name

Carl G de Boer

Organization name

The Broad Institute

Lab

Aviv Regev

Street address

415 Main St