|
| Status |
Public on Jun 15, 2016 |
| Title |
rip_DMSO_replicate1 [Sample 16] |
| Sample type |
SRA |
| |
|
| Source name |
HEK 293 T-Rex_rip_DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK 293 T-REx cell
genotype/variation: stabley expressing SBP-tagged eIF4A
treatment: DMSO
molecule: total RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard mRNA-seq
TRI-reagent (sigma) and following Direct-zol RNA-MiniPrep (zymo research).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
For Ribosome profiling, mRNA-Seq, and RIP-Seq:
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 (amino acid) used for read counting;3. read counts
For Bind-n-Seq:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Depleting duplicated reads with Fast-X-toolkit
Supplementary_files_format_and_content: The fasta file was made by FASTX-Tool kit FASTA/Q Collapser, to eliminate duplicated sequence. Sequence is named with two number, a running number followed by how many times that sequence occurred.
|
| |
|
| Submission date |
Jun 24, 2015 |
| 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 |
GPL11154 |
| Series (1) |
| GSE70211 |
Rocaglamide A converts RNA helicase eIF4A into a sequence-specific translational repressor |
|
| Relations |
| BioSample |
SAMN03788122 |
| SRA |
SRX1070873 |
