|
| Status |
Public on Jul 31, 2017 |
| Title |
rqt1_control2 |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
treatment: p416GPDp-GFP-FLAG-HIS3
genetic background: MATa ade2 his3 leu2 trp1 ura3 can1, hel2∆::natMX4
cell line: hel2-delta
extracted molecule: total RNA
extract_protocol: Rnase I footprinting, ribosome pelleting, RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification
Ribosome profiling
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Ribosome Profiling
|
| Data processing |
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-FLAG-HIS3 or p416GPDp-GFP-R12-FLAG-HIS3
Read quantitation using custom scripts
Genome_build: p416GPDp-GFP-FLAG-HIS3 and 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 |
Mar 25, 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) |
| GSE79622 |
Ubiquitination of Stalled Ribosome Triggers Ribosome-associated Quality Control [SET1] |
| GSE90920 |
Ubiquitination of Stalled Ribosome Triggers Ribosome-associated Quality Control |
|
| Relations |
| BioSample |
SAMN04580390 |
| SRA |
SRX1663377 |
