|
| Status |
Public on May 01, 2024 |
| Title |
set2_NACER_ASO |
| Sample type |
SRA |
| |
|
| Source name |
Huh7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Huh7
genotype/variation: NACER
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell homogenates using Trizol.
A library was prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA LT Sample Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
set2_NACER_ASO_1
|
| Data processing |
Built-in software (HCS 2.2.70) was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.5 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.32, then mapped to hg19 whole genome using HISTAT2 v2.0.5 and Bowtie2 v2.2.6
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v1.3.3b.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample
|
| |
|
| Submission date |
Jun 06, 2018 |
| Last update date |
May 01, 2024 |
| Contact name |
Sang Geon Kim |
| E-mail(s) |
sgk@snu.ac.kr
|
| Phone |
+82-2-880-7840
|
| Organization name |
Seoul National University
|
| Department |
College of Pharmacy
|
| Lab |
Lab of Molecular Pharmacology
|
| Street address |
San56-1, Sillim-dong, Kwanak-gu
|
| City |
Seoul |
| State/province |
Seoul |
| ZIP/Postal code |
151-742 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE115409 |
NACER, a liver-specific lncRNA, functions as Nrf2-activating competing endogenous RNA for Plk2 and p21cip1 |
|
| Relations |
| BioSample |
SAMN09375110 |
| SRA |
SRX4174664 |
