|
| Status |
Public on Sep 23, 2015 |
| Title |
ribo_ND3_shControl_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
hES cell, treated with sh control, ND 3d
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: lentiviral infection with sh control
cell line: H1
extract_protocol: Rnase I footprinting, ribosome pelleting, RNA extraction
|
| Growth protocol |
neural conversion with NIM for 3d
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: Ribosome Profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie2 v2.0.6
Transcriptome alignment with TopHat v2.0.7
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 |
Oct 10, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Shintaro Iwasaki |
| E-mail(s) |
[email protected]
|
| 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 |
GPL11154 |
| Series (1) |
| GSE62247 |
Cell fate determination by ubiquitin-dependent regulation of translation |
|
| Relations |
| BioSample |
SAMN03104428 |
| SRA |
SRX730875 |
