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Sample GSM3395672 Query DataSets for GSM3395672
Status Public on Feb 01, 2019
Title N-lim_rep3 MC Hap1-tagged
Sample type SRA
 
Source name MC
Organism Saccharomyces cerevisiae
Characteristics strain: HAP1-TAP constructed from CEN.PK 113-5D by adding a C-terminal CBP-ProtA tag to Hap1p
carbon source: 6% (w/v) glucose
Growth protocol Cells were cultivated in four different limited media in chemostat: n-lim, glu-lim, et-lim and oxy.glu-lim
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Counts_table.xlsx
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
 
Submission date Sep 19, 2018
Last update date Feb 01, 2019
Contact name David Bergenholm
E-mail(s) [email protected]
Phone 703538155
Organization name Chalmers tekniska högskola
Street address Axgatan 139
City Mölndal
State/province SWEDEN
ZIP/Postal code 43140
Country Sweden
 
Platform ID GPL19756
Series (1)
GSE120188 Construction of Mini-Chemostats for High-throughput Strain Characterization
Relations
BioSample SAMN10092754
SRA SRX4717017

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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