|
Status |
Public on Jun 15, 2016 |
Title |
iclip_RocA3 |
Sample type |
SRA |
|
|
Source name |
HEK 293 T-REx cell
|
Organism |
Homo sapiens |
Characteristics |
treatment: RocA 3 uM cell line: HEK 293 T-REx cell extracted molecule: total RNA extract_protocol: Partial Rnase I digestion, SBP-tag purification, RNA extraction
|
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 4000 |
|
|
Description |
iCLIP-Seq
|
Data processing |
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 Depleting duplicated reads with Fast-X-toolkit fasta files, reads named with "id number" - "duplication number of the read"
|
|
|
Submission date |
Mar 18, 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 |
GPL20301 |
Series (1) |
GSE79392 |
Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor |
|
Relations |
BioSample |
SAMN04568456 |
SRA |
SRX1642576 |