|
| Status |
Public on May 21, 2019 |
| Title |
SK 20 24h rep2 |
| Sample type |
SRA |
| |
|
| Source name |
SK-N-BE(2) neuroblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 20 mM ethanol
timepoint: 24 h
tissue: brain
cell line: SK-N-BE(2)
cell type: neuroblastoma
gender: male
age: 2 years
|
| Treatment protocol |
24h and 42h incubation with 10 mM and 20 mM ethanol
|
| Growth protocol |
1:1 mixture of EMEM and F12K with 10% fetal bovine serum and 1% penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted with QIAgen Rneasy, samples prepped with TruSeq RNA Library Pre Kit v2
Libraries prepared according to Illumina protocols for HiSeq 4000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base-calling by default HiSeq 4000 settings
Reads mapped to hg38 by STAR (v2.5) using parameter “--outSAMmapqUnique 60”
Features counted by featureCounts (from subread v1.5.3) using parameters “-s 2 -p -Q 10”
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files contain raw counts from featureCounts
|
| |
|
| Submission date |
May 20, 2019 |
| Last update date |
May 21, 2019 |
| Contact name |
Andy Chen |
| E-mail(s) |
andychen@iupui.edu
|
| Organization name |
IUSM
|
| Department |
MMGE
|
| Street address |
410 W 10th Street, Suite 5000
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE131470 |
Expression analysis of ethanol treatment on SK-N-BE(2) |
|
| Relations |
| BioSample |
SAMN11783979 |
| SRA |
SRX5865796 |
