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| Status |
Public on Dec 07, 2020 |
| Title |
375_DMSO2 |
| Sample type |
SRA |
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| Source name |
Rnase I footprinting, ribosome pelleting, RNA extraction
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| Organism |
Homo sapiens |
| Characteristics |
treatment: DMSO
genetic background: WT
cell line: A375
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| Treatment protocol |
DMSO or RocA for 30min
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Ribosome Profiling
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| Data processing |
Library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with bowtie2 v2.1.0
Alignment with TopHat v2.0.9
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts
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| Submission date |
Apr 14, 2020 |
| Last update date |
Dec 07, 2020 |
| Contact name |
Mingming Chen |
| E-mail(s) |
mingming.chen@riken.jp
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| Phone |
07031428686
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| Organization name |
RIKEN
|
| Department |
CPR
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| Lab |
RNA systems biochemistry lab
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| Street address |
Hirisawa 2-2
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| City |
Wakoshi |
| State/province |
Saitama |
| ZIP/Postal code |
351-0106 |
| Country |
Japan |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE148636 |
Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A |
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| Relations |
| BioSample |
SAMN14596016 |
| SRA |
SRX8112246 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4475943_375_DMSO2.txt.gz |
868.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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