|
| Status |
Public on Apr 15, 2017 |
| Title |
LkPHO4 pho2Δ replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
OD600=0.3~0.5 log-phase yeast culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
pho80 locus: pho80delta
pho2 locus: pho2delta
pho4 locus: L. kluyveri PHO4
|
| Treatment protocol |
NA
|
| Growth protocol |
Cells were pre-grown in 10 mM Pi Synthetic Complete (SC) medium to saturation, diluted 1:100 and regrown to saturation. The culture is then diluted to OD600 ~ 0.1 in fresh 10 mM Pi SC medium and grown to OD600 ~ 0.3-0.5 prior to extraction
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
20 mL of OD600=0.3-0.5 cell cultures were added directly into 30 mL cold methanol (-50 °C), mixed, and incubated in an ethanol-dry ice bath (-50 °C) for at least 20 minutes. Cells were collected by centrifugation and quickly washed with ice-cold water to remove alcohol, and resuspended in RNAlater solution (Ambion). For each sample, 5×107 cells were used to isolate total RNA with the RNase Mini kit (Qiangen),
RNA libraries were prepared using the Illumina TruSeq stranded mRNA library preparation kit (part #RS-122-2101 and #RS-122-2102) following the manufacturer’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
H1a
|
| Data processing |
Basecalling using bcl2fastq-1.8.3
Sequencing reads were aligned to the corresponding species reference genome using Bowtie (v1.1.1) with the option ‘-m 1 --best –strata’
The resulting SAM files were sorted using Samtools (v1.2)
The number of reads per transcript was counted using Bedtools2, with the option ‘bedtools coverage -a BAM_file -b genome_annotation.bed -S -s sorted -g Chrom.length`. Gene features for S. cerevisiae were downloaded from the Saccharomyces Genome Database (SGD), version R64-2-1.
Genome_build: S. cerevisiae genome version S288C_R64-1-1
Supplementary_files_format_and_content: text file, matrix of read counts per transcript per strain
|
| |
|
| Submission date |
Apr 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bin He |
| E-mail(s) |
emptyhb@gmail.com, bin-he@uiowa.edu
|
| Organization name |
the University of Iowa
|
| Department |
Biology
|
| Lab |
Gene Regulatory Evolution
|
| Street address |
129 East Jefferson St., Biology Building 450
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE97799 |
Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Scer RNA-seq] |
| GSE97801 |
Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway |
|
| Relations |
| BioSample |
SAMN06756849 |
| SRA |
SRX2737309 |
