|
Status |
Public on Jul 31, 2017 |
Title |
us10kr_control1 |
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, rps20::natMX4, p415-rps20K6/8R cell line: rps20-delta, p415-RpS20K6/8R 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 |
SAMN04580395 |
SRA |
SRX1663382 |