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Sample GSM3362041 Query DataSets for GSM3362041
Status Public on Aug 29, 2020
Title cglab wt_C
Sample type SRA
 
Source name Yeast culture (BMW) - log phase
Organism Nakaseomyces glabratus
Characteristics genotype: wild type
replicate: C
growth phase: log
Treatment protocol NA
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 Cgla.OG.logFC.txt.gz
Cgla.Gene.logFC.txt.gz
RNA-seq for wild type Candida glabrata in Yeast culture (BMW) - log phase (log), replicateC. Used to generate column Cgla_0682_Log and Cgla_9955_Log in Cgla.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
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL22622
Series (2)
GSE119237 SFP1 (RNA-seq)
GSE119238 The roles of duplication and divergence in the evolution of a transcription factor
Relations
BioSample SAMN09936882
SRA SRX4624569

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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