|
| Status |
Public on Sep 26, 2013 |
| Title |
mRNA-seq for wildtype |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: S288C
strain genotype: BY4743
|
| Growth protocol |
1 liter of Homozygous diploid wildtype or whi3 cells was grown in 1L YPED to log phase. Upon harvest, culture was pour onto ice and cyclohexamide mixture (the final concentration of cycloheximide was 100 µg/ml) Cells were washed once with ice cold water with 100 µg/ml cycloheximide before RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ribosome footprint and small mRNA fragment are prepared using the ARTseq™ Ribosome Profiling Kit (CAT# RPYSC12116) following manufacturer's instructions.
Libraries were prepared using the ARTseq™ Ribosome Profiling Kit (CAT# RPYSC12116) following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
poly(A) tail RNA
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Tools from fastx were used to trimmed reads to 27 nucleotides and filtered with parameters –Q 33 –q 30 –p 85.
The first 26 nucleotide of the resulted reads were aligned against S288C reference genome R64 using bowtie2 with the end-to-end alignment method and the minimum score was set to -7. Unaligned reads were recycled for additional alignment using coding region sequence as reference to retrieve exon junction reads.
The position of the 5’ end in the read was used to assign reads to genomic features according to (Ingolia N et al Science 2009) Reads mapped to the rDNA were discarded for following analysis. Reads per kilo base per Million (RPKM) was calculated to quantify mRNA and ribosomal footprints. Briefly, after removal of genes with less than 7 reads, the count of reads for each gene was normalized by its length (in kb) and the total number of reads (in million).
Genome_build: S288C_reference_genome_R64-1-1
Supplementary_files_format_and_content: RPKM values for each sample
|
| |
|
| Submission date |
Sep 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ying Cai |
| E-mail(s) |
cai.ying@stonybrook.edu
|
| Organization name |
Stony Brook University
|
| Department |
Molecular Genetics and Microbiology
|
| Lab |
Bruce Futcher
|
| Street address |
Life Sciences Building Rm 363
|
| City |
Stony Brook |
| State/province |
New York |
| ZIP/Postal code |
11794 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN02363924 |
| SRA |
SRX360296 |
