|
| Status |
Public on Dec 09, 2017 |
| Title |
dcp2-N245-198Q-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SYY2755
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
background: W303
genotype: dcp2-E198Q-N245::KanMX6
time: experiment at time period II
|
| Growth protocol |
Cells were all grown in YEPD media at 30°C. In each case, cells (15 ml) were grown to an OD600 of 0.7 and harvested by centrifugation. Cell pellets were frozen on dry ice and then stored at -80°C until RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from yeast cells using hot phenol.
Total RNA was treated with Baseline-zero DNase (Epicenter, cat# DB0711K) to remove any genomic DNA contamination. Five micrograms of DNase-treated total RNA was then depleted of rRNAs using the Illumina yeast RiboZero Removal Kit (cat# MRZY1306) and the resulting RNA was used for RNA-Seq library preparation. Multiplex strand-specific cDNA libraries were constructed using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (cat# RS-122-2101).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
wt_198q_expressions.txt
|
| Data processing |
RSEM program (Li and Dewey 2011) was used to map the sequence reads to the transcriptome and to quantify individual transcript levels with settings --bowtie-m 30 --no-bam-output --forward-prob 0.
The expected read counts for individual transcripts from RSEM were considered as the number of reads mapped to each transcript and were then imported into Bioconductor DESeq package (Anders and Huber 2010) for differential expression analysis.
Genome_build: R64-2-1 S288C sacCer3 genome assembly
Supplementary_files_format_and_content: Tab-delimited text files include the estimated read counts (normalized abundance estimates) of individual transcripts in wild-type cells and in each of the mutant strains
|
| |
|
| Submission date |
Dec 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Feng He |
| E-mail(s) |
feng.he@umassmed.edu
|
| Phone |
508-856-3931
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Microbiology and Physiological Systems
|
| Street address |
368 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01655 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE107841 |
Genome-wilde identification of decapping substrates in the yeast Saccharomyces cervisiae |
|
| Relations |
| BioSample |
SAMN08150061 |
| SRA |
SRX3458826 |
