|
Status |
Public on Apr 15, 2017 |
Title |
pho4Δ 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: pho4delta
|
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 |
D1a
|
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 |
SAMN06756882 |
SRA |
SRX2737293 |