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| Status |
Public on Feb 01, 2019 |
| Title |
N-lim_rep1 MC WT |
| Sample type |
SRA |
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| Source name |
MC
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: CEN.PK 113-5D
carbon source: 6% (w/v) glucose
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| Growth protocol |
Cells were cultivated in four different limited media in chemostat: n-lim, glu-lim, et-lim and oxy.glu-lim
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells cultivated in chemostats were sampled for RNA-seq analysis after steady state was achieved(OD600, dissolved oxygen and off-gas profiles became constant) for 48 to 60 hours. Rapidly withdrawing 10 OD of culture and put into a precooled 50 ml falcon tube, the samples were immediately centrifuged at 4000 rpm for 5 min at −20 °C. The supernatant was discarded, the pellet was frozen in liquid nitrogen and stored at −80 °C until further analysis. The RNA extraction was performed using the RNeasy Mini Kit (QIAGEN).
The sequencing libraries were prepared in three replicates using a TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold, RS122-2303, + Ribo-Zero magnetic Gold Kit from Epicentre
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Counts_table.xlsx
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| Data processing |
RNA sequencing reads (R1 & R2 reads) were mapped to reference genome assembly with Bowtie2 using default settings to generate SAM files.
SAM files were treated with SAMtools option –q 20 to remove low-quality reads and then converted to sorted BAM files.
Bedtools Genomcov function was used to generate read counts
Genome_build: R64-2-1 of S. cerevisiae S288C
Supplementary_files_format_and_content: Excel .xlsx file containing Systematic name, common name, three lines of raw reads, three lines of CPM, one line for mean and one for std, this was done for all conditions and all experiments
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| Submission date |
Sep 19, 2018 |
| Last update date |
Feb 01, 2019 |
| Contact name |
David Bergenholm |
| E-mail(s) |
[email protected]
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| Phone |
703538155
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| Organization name |
Chalmers tekniska högskola
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| Street address |
Axgatan 139
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| City |
Mölndal |
| State/province |
SWEDEN |
| ZIP/Postal code |
43140 |
| Country |
Sweden |
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| Platform ID |
GPL19756 |
| Series (1) |
| GSE120188 |
Construction of Mini-Chemostats for High-throughput Strain Characterization |
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| Relations |
| BioSample |
SAMN10092774 |
| SRA |
SRX4717027 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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