|
| Status |
Public on Oct 06, 2017 |
| Title |
LA18_3 |
| Sample type |
SRA |
| |
|
| Source name |
yeast cells
|
| Organism |
Zygosaccharomyces parabailii |
| Characteristics |
strain: ATCC60483
condition: Lactic acid treated
timepoint, hours: 18 h
|
| Growth protocol |
Batch bioreactor fermentation was performed in Verduyn medium at pH 3 with addition of 40 g L^ -1 lactic acid or without lactic acid. The samples for RNA sequencing were taken at 18 h and 42 h, corresponding to exponential phase and post diauxic shift
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was then extracted using Zymo Research Fungal/Bacterial RNA MiniPrep™ kit (Irvine, USA) and the quality of RNA samples were evaluated with Agilent Bioanalyzer. The RNA samples were sequenced using the Illumina HiSeq2000 platform with 100 nt-long paired-end reads
Library construction using Illumina Truseq RNA protocol after rRNA depletion.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Lactic acid treated at 18 h rep3
Sample_9
|
| Data processing |
The datasets were generated from a hybrid organism. The genome of this organism contains two similar copies for almost every gene originated from the two parental strains. Some of these genes are identical duplicated genes whose predicted functions are important for the phenotype analysed in this study. In order to analyse their expression profiles, the alignments reported by bowtie were filtered from the SAM files by the "multimapping" XM:i:2 for which the mapping quality (MAPQ) is artificially set to 0. Those alignments were used to produce counts only for the duplicated genes by setting the htseq-count quality filter to 0 (-a 0). These are referred as "Dups".
Setting the htseq-count quality filter to 0 using the full set of alignments over the full genome would have produced counts from low quality alignments which do not necessarily include the tag XM:i:2. To avoid that, a second run was performed with the default htseq-count quality filter (MAPQ >= 10) and produced the "Full" datasets which have 0 counts for the above mentioned duplicated genes.
Full and Dup: Read mapping using bowtie v1.1.2 ; parameters -v 0 -k 10 --best -M 1
Full: htseq-count v0.6.0
Full: edgeR v. 3.18.1 trimmed means of M-values (TMM) normalization and counts per million (CPM) calculation; removed genes with less than 1 CPM in at least 3 samples from the same condition.
Dups: Read mapping using bowtie v1.1.2 ; parameters -v 0 -k 10 --best -M 1
Dups: samtools v0.1.19-44428cd ; parameters view -bF 4 - | grep XM:i:2
Dups: htseq-count v0.6.0 -a 0
Dups: edgeR v. 3.18.1 trimmed means of M-values (TMM) normalization and counts per million (CPM) calculation; removed genes with less than 1 CPM in at least 3 samples from the same condition.
Dups: edgeR v. 3.18.1 Reads Per Kilobase of transcript per Million mapped reads (RPKM) calculation using the normalized and filtered "Dups" dataset.
Genome_build: Zygosaccharomyces parabailii (assembly ASM198439v2)
Supplementary_files_format_and_content:
Zpar_Full_counts.map.txt: Merged htseq-count text file
Zpar_Full_matrix.txt: Filtered and normalized Zpar_Full CPMs
Zpar_Dups_counts.map.txt: Merged htseq-count text file
Zpar_Dups_matrix.txt: Filtered and normalized Zpar_Dups CPMs
Zpar_Dups_RPKMs.txt: RPKMs for the filtered and normalized Zpar_Dups set
|
| |
|
| Submission date |
Oct 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Raúl Antonio Ortiz-Merino |
| E-mail(s) |
[email protected]
|
| Organization name |
Delft University of Technology
|
| Department |
Biotechnology
|
| Lab |
Industrial Microbiology
|
| Street address |
van der Maasweg 9
|
| City |
Delft |
| ZIP/Postal code |
2629 HZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24086 |
| Series (1) |
| GSE104654 |
Transcriptional response to lactic acid stress in the hybrid yeast Zygosaccharomyces parabailii |
|
| Relations |
| BioSample |
SAMN07741608 |
| SRA |
SRX3254915 |
