|
| Status |
Public on Nov 19, 2022 |
| Title |
2B-NNK cells,NNK treatment 2 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: lung
cell line: BEAS-2B
cell type: epithelial cell
genotype: WT
treatment: NNK treatment
|
| Treatment protocol |
Cells were seeded in 6-well plates containing 100 mg/L NNK and cultured for 24 h every 4 d. Finally, the total amount of NNK processed was 1mg.
|
| Growth protocol |
BEAS-2B and 2B-NNK cells were maintained in BEBM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) . 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit(Illumina) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
hisat2 v 2.1.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v 1.17 (parameter- Mapped: 0.85)
Trimmed sequence reads were mapped to GRCh37 using hisat2
Read count extractionwas performed using hisat2.
Read count normalization was performed using R package "Ballgown".
Assembly: GRCh37
Supplementary files format and content: matrix table files include FPKM values for each Sample
|
| |
|
| Submission date |
Nov 15, 2022 |
| Last update date |
Nov 19, 2022 |
| Contact name |
qiaoyuan yang |
| E-mail(s) |
yqy1208@126.com
|
| Phone |
+86 13697414042
|
| Organization name |
Guangzhou Medical University
|
| Street address |
Xinzao Town, Panyu District
|
| City |
Guangzhou |
| ZIP/Postal code |
511436 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE217991 |
Chimeric RNA RRM2-C2orf48 plays an oncogenic role in the development of NNK-induced lung cancer |
|
| Relations |
| BioSample |
SAMN31727459 |
| SRA |
SRX18271971 |
