|
| Status |
Public on Mar 01, 2019 |
| Title |
CAL_62_THZ1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Anaplastic thyroid carcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Thyroid
tissue type: Anaplastic thyroid carcinoma
cell line: CAL-62
treatment: THZ1
|
| Treatment protocol |
BCPAP cells and CAL-62 cells were treated with 100 nM THZ1 for 6 h
|
| Growth protocol |
BCPAP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. CAL-62 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) medium supplemented with 20% fetal bovine serum (FBS). All cells were maintained at 37°C in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from cultured cells were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Low quality reads was filtered using internal software SOAPnuke
Clean reads were mapped to reference using Bowtie2. Only unique mapped reads were used in further analysis.
DEGs (differential expressed genes) between samples were generated by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.
|
| |
|
| Submission date |
Sep 19, 2018 |
| Last update date |
Mar 01, 2019 |
| Contact name |
Xinyi Cao |
| E-mail(s) |
cxyldd@tmu.edu.cn
|
| Phone |
86-22-83336728
|
| Organization name |
Collaborative Innovation Center of Tianjin for Medical Epigenetics
|
| Street address |
Tianjin Medical University No.22 Qixiangtai Road
|
| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (2) |
| GSE120176 |
Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer [RNA-Seq] |
| GSE120177 |
Targeting super-enhancer-driven oncogenic transcription by CDK7 inhibition in anaplastic thyroid cancer |
|
| Relations |
| BioSample |
SAMN10092262 |
| SRA |
SRX4715708 |
