|
| Status |
Public on Jul 31, 2017 |
| Title |
rqt1_R12_2 |
| Sample type |
SRA |
| |
|
| Source name |
rqt1_R12
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genetic background: MATa ade2 his3 leu2 trp1 ura3 can1, hel2<delta>::natMX4
cell line: hel2<delta>
treated with: p416GPDp-GFP-R12-FLAG-HIS3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rnase I footprinting, ribosome pelleting, RNA extraction
Trizol and following Direct-zol kit (Zymo scientific).
RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Ribosome Profiling
|
| Data processing |
library strategy: ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA alignment with bowtie2 v2.0.6
Alignment with TopHat v2.0.7 to reporter plasmid p416GPDp-GFP-R12-FLAG-HIS3
Read quantitation using custom scripts
Genome_build: p416GPDp-GFP-R12-FLAG-HIS3
Supplementary_files_format_and_content: text files contain following columns: 1.distance from start codon [nt] ;2-36. total or 13 to 36 nucleotides long reads at the given position. Asite positions of the reads are asigned.
|
| |
|
| Submission date |
Dec 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shintaro Iwasaki |
| E-mail(s) |
shintaro.iwasaki@riken.jp
|
| Organization name |
RIKEN
|
| Department |
Cluster for Pioneering Research
|
| Street address |
S205 Bioscience Bldg. 2-1 Hirosawa
|
| City |
Wako |
| State/province |
Saitama |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21656 |
| Series (2) |
| GSE90919 |
Ubiquitination of Stalled Ribosome Triggers Ribosome-associated Quality Control [SET2] |
| GSE90920 |
Ubiquitination of Stalled Ribosome Triggers Ribosome-associated Quality Control |
|
| Relations |
| BioSample |
SAMN06111898 |
| SRA |
SRX2396726 |
