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Sample GSM2094330 Query DataSets for GSM2094330
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

Supplementary file Size Download File type/resource
GSM2094330_iclip_RocA3.fa.gz 12.2 Mb (ftp)(http) FA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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