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Sample GSM1720812 Query DataSets for GSM1720812
Status Public on Jun 15, 2016
Title rna_RocA3 [Sample 10]
Sample type SRA
 
Source name HEK 293 T-Rex_rna_RocA3
Organism Homo sapiens
Characteristics cell line: HEK 293 T-REx cell
treatment: RocA 3 uM
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 RNA-Seq
Library source transcriptomic
Library selection cDNA
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 SAMN03788116
SRA SRX1070867

Supplementary file Size Download File type/resource
GSM1720812_rna_RocA3.txt.gz 401.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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