|
| Status |
Public on Dec 30, 2018 |
| Title |
ribo_naive_roca |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T-REx
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: RocA treatment
cell line: HEK293T-REx
extracted molecule: total RNA
extract_protocol: Rnase I footprinting, ribosome pelleting, RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction, preadenylated linker ligation, rRNA depeletion, 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 and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: hg19
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts
|
| |
|
| Submission date |
Aug 16, 2017 |
| 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 |
GPL20301 |
| Series (1) |
| GSE102720 |
Ternary protein•drug•RNA interface explains RocA sequence selectivity and Aglaia resistance |
|
| Relations |
| BioSample |
SAMN07513443 |
| SRA |
SRX3097576 |
