|
| Status |
Public on Jan 24, 2017 |
| Title |
DMS-MapSeq_WT_replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain (genetic background): wild-type DED1
temperature: 37 dgC for 5 min
molecule type: mRNA
|
| Treatment protocol |
Cells were treated with dimethyl sulfate (5% (v/v) final concentration) prior to harvesting
|
| Growth protocol |
Cells were grown to an OD600 of ~ 0.6 in YPD medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were rapidly sedimented and snap-frozen on dry ice. Whole cell extracts were generated by breaking the cells with glass beads.
Detailed information available in the Methods section of the article.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
replicate 1
total_DMSMapSeq_norm_WT5_normCounts.txt
|
| Data processing |
Basecalling with Illumina Casava software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie
Transcriptome alignment with TopHat
Further read analyses by custom scripts in Rstudio
More detailed information on additonal software in the methods section of the accompanying article.
Genome_build: sacCer3
Supplementary_files_format_and_content: mRNACo quantification in .tabular format (columns 1-13:tracking_id:1; class_code:2; nearest_ref_id:3; gene_id:4; gene_short_name:5; tss_id:6; locus:7; length:8; coverage:9; FPKM:10; FPKM_conf_lo:11; FPKM_conf_hi:12; FPKM_status:13); all other data files in .txt format (columns 1-7: chr:7; position:2; strand:3; sequence:4; gene:5; gene feature:6; normalized counts)
|
| |
|
| Submission date |
Jan 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ulf-Peter Guenther |
| Organization name |
Case Western Reserve University
|
| Department |
Biochemistry/ RNA Center
|
| Lab |
Jankowsky
|
| Street address |
10900 Euclid Ave
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE93959 |
The RNA helicase Ded1p suppresses translation initiation from near-cognate start codons |
|
| Relations |
| BioSample |
SAMN06251047 |
| SRA |
SRX2511477 |
