|
| Status |
Public on May 28, 2018 |
| Title |
LR-LBH-1_miRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
H3122 lung cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H3122
treatment: Certinib + Panobinostat
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the mirVana miRNA isolation kit (Ambion).
Small RNAs (20 - 30 nt) were purified from 15% Novex TBE-Urea gel (Invitrogen) and ligated first with the 5’ RNA adaptor and then with the 3’ RNA adaptor provided by Illumina TruSeq small RNA sample preparation protocol. In each step, the ligated product was PAGE-gel purified. After first-strand synthesis and 11 cycles of PCR amplification, the product was PAGE-gel purified.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base calling was performed by Illumina Genome Studio(V2010.1).
After TruSeq small RNA adapters were eliminated among the sequenced reads by Trimommatic software (v.0.33), the remained sequence data were mapped to the human genome (hg19) using bowtie2 (v.2.2.2).
The quantification of each miRNA was estimated using HTSeq software package.
Then, the fragments
per
kilobase
of
transcript
per
million
fragments
mapped (FPKM) of each sample was estimated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text format with FPKM values of miRNA
|
| |
|
| Submission date |
May 16, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Seon-Kyu Kim |
| E-mail(s) |
seonkyu@kribb.re.kr
|
| Phone |
+82-42-879-8107
|
| Organization name |
Korea Research Institutue of Bioscience & Biotechnology
|
| Department |
Personalized Genomic Medicine Research Center
|
| Street address |
125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Korea
|
| City |
Daejeon |
| ZIP/Postal code |
305-806 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE81486 |
Expression profiling by small RNA-seq for identifying miRNA associated with epithelial-mesenchymal transition and acquired resistance to ALK inhibitors |
| GSE81487 |
Epithelial-mesenchymal transition and acquired resistance to ALK inhibitors |
|
| Relations |
| BioSample |
SAMN05003690 |
| SRA |
SRX1769354 |
