|
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.
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|
|
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 |