Defining the transcriptional landscape of Candida glabrata by RNA-Seq

RNA-seq We study the transcriptional landscape of C. glabrata and identify differentially expressed genes between pH4 and ph8 as well as between nitrosative stress (GSNO) treatment and controll. Candida glabrata was grown in standard nutrient-rich medium, ph4, ph8 and in GSNO conditions. Paired-end and strand-specific RNA-Seq was performed on three biological replicates after PolyA filtering. A fourth replicate without filtering was sequenced single-end and not strand-specific.

Experiment Design: growth_condition_design Experimental Factor: Oxygen Stress, Medium, pH Experimental Factor Type: compound, media, pH Quality Control Type: biological_replicate Public Release Date: 2015-01-27 Database ID: GEO Accession Number: GSE61606

Protocol Name Software Name COUNTING htseq-count DIFFERENTIAL EXPRESSION FILTERING DESeq QUALITY CONTROL OF RAW DATA FastQC QUALITY TRIMMING OF RAW DATA btrim MAPPING tophat2

Specimen Extract Name 260/280 230/280 RIN/RNA Integrity Number Concentration Concentration Unit Volume Volume Unit Extraction Kit Material Type Extraction Date wt_pH4_4 wt_pHa_4_e 9.6 100 µg/µl 50 µl RNA extraction kit total_RNA 2012-12-05 wt_pH8_4 wt_pHb_4_e 9.7 100 µg/µl 50 µl RNA extraction kit total_RNA 2012-12-05 wt_pH4_1 wt_pHa_1_e 9.8 100 µg/µl 50 µl RNA extraction kit total_RNA 2012-12-05 wt_pH4_2 wt_pHa_2_e 9.8 100 µg/µl 50 µl RNA extraction kit total_RNA 2012-11-21 wt_pH4_3 wt_pHa_3_e 9.7 100 µg/µl 50 µl RNA extraction kit total_RNA 2012-11-15 wt_pH8_1 wt_pHb_1_e 9.5 100 µg/µl 50 µl RNA extraction kit total_RNA 2012-12-05 wt_pH8_2 wt_pHb_2_e 10 100 µg/µl 50 µl RNA extraction kit total_RNA 2012-11-21 wt_pH8_3 wt_pHb_3_e 9.9 100 µg/µl 50 µl RNA extraction kit total_RNA 2012-11-15 wt_GSNO_1 wt_GSNO_1_e 100 µg/µl 50 µl RNA extraction kit total_RNA wt_GSNO_2 wt_GSNO_2_e 100 µg/µl 50 µl RNA extraction kit total_RNA wt_GSNO_3 wt_GSNO_3_e 100 µg/µl 50 µl RNA extraction kit total_RNA wt_GSNO_4 wt_GSNO_4_e 100 µg/µl 50 µl RNA extraction kit total_RNA wt_37_1 wt_37_1_e 100 µg/µl 50 µl RNA extraction kit total_RNA wt_37_2 wt_37_2_e 100 µg/µl 50 µl RNA extraction kit total_RNA wt_37_3 wt_37_3_e 100 µg/µl 50 µl RNA extraction kit total_RNA wt_37_4 wt_37_4_e 100 µg/µl 50 µl RNA extraction kit total_RNA

Specimen Assay Name Performer Technology Type Sequencing Instrument Library Source Library Strategy Library Selection Library Layout Sequencing Date wt_pH4_4 wt_pHa_4_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic single end; unspecific; no poly-A filter random single 2012-12-05 wt_pH8_4 wt_pHb_4_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic single end; unspecific; no poly-A filter random single 2012-12-05 wt_pH4_1 wt_pHa_1_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single 2012-12-05 wt_pH4_2 wt_pHa_2_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single 2012-11-21 wt_pH4_3 wt_pHa_3_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single 2012-11-15 wt_pH8_1 wt_pHb_1_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single 2012-12-05 wt_pH8_2 wt_pHb_2_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single 2012-11-21 wt_pH8_3 wt_pHb_3_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single 2012-11-15 wt_GSNO_1 wt_GSNO_1_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single wt_GSNO_2 wt_GSNO_2_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single wt_GSNO_3 wt_GSNO_3_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single wt_GSNO_4 wt_GSNO_4_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic single end; unspecific; no poly-A filter random single wt_37_1 wt_37_1_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single wt_37_2 wt_37_2_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single wt_37_3 wt_37_3_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic paired end; strand specific; poly-A filter random single wt_37_4 wt_37_4_s GATC Biotech Sequencing by synthesis (Illumina) Illumina HiSeq 2000 genomic single end; unspecific; no poly-A filter random single

Specimen Material Type Organism Strain or Line Organism Part Organism Status Sex Age Age Time Unit Sampling Time Point Sampling Time Point Unit Temperature Temperature Unit pH Atmosphere Compound Media Nutrients Fold Change Assignment Name Fold Change Assignment Feature wt_pH4_4 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C 4 air none M199 none pH4_VS_pH8 control wt_pH8_4 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C 8 air none M199 none pH4_VS_pH8 treatment wt_pH4_1 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C 4 air none M199 none pH4_VS_pH8 control wt_pH4_2 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C 4 air none M199 none pH4_VS_pH8 control wt_pH4_3 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C 4 air none M199 none pH4_VS_pH8 control wt_pH8_1 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C 8 air none M199 none pH4_VS_pH8 treatment wt_pH8_2 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C 8 air none M199 none pH4_VS_pH8 treatment wt_pH8_3 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C 8 air none M199 none pH4_VS_pH8 treatment wt_GSNO_1 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C air GSNO YPD none GSNO_VS_NONE treatment wt_GSNO_2 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C air GSNO YPD none GSNO_VS_NONE treatment wt_GSNO_3 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C air GSNO YPD none GSNO_VS_NONE treatment wt_GSNO_4 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C air GSNO YPD none GSNO_VS_NONE treatment wt_37_1 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C air none YPD none GSNO_VS_NONE control wt_37_2 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C air none YPD none GSNO_VS_NONE control wt_37_3 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C air none YPD none GSNO_VS_NONE control wt_37_4 whole_organism Candida glabrata CBS138 (ATCC 2001) all fresh not applicable 0 hour(s) 0 hour(s) 37 degrees_C air none YPD none GSNO_VS_NONE control