|
| Status |
Public on Mar 05, 2021 |
| Title |
KYSE180_siTP63_1 |
| Sample type |
SRA |
| |
|
| Source name |
Esophageal squamous cell carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ESCC cell line KYSE180
genotype: p63 Knock-down
|
| Treatment protocol |
Cells were transfected with siRNAs or plasmids as indicated.
|
| Growth protocol |
KYSE180 and TE6 were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% Penicillin and Streptomycin. KYSE150 cells were RPMI-1640 medium supplemented with 5% FBS, 1% Penicillin and Streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using QIAzol lysis reagent according to the manufacturer's manual.
RNA-seq libraries were constructed using Illumina TruSeq RNA library prep kit V2 according to the manufacturer’s manual.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
KYSE180_TP63_KD_normCounts.txt
|
| Data processing |
Alignment was done using STAR (2.6.0).
Feature counting was performed using HTSeq (0.11.2).
Differential gene analysis and counts normalization were done using DEseq2 (1.24.0).
Genome_build: hg38
Supplementary_files_format_and_content: Text files containing gene counts matrix.
|
| |
|
| Submission date |
Jul 27, 2020 |
| Last update date |
Mar 05, 2021 |
| Contact name |
Xin Wang |
| E-mail(s) |
x.wang@siat.ac.cn
|
| Organization name |
Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
|
| Department |
Institute of Synthetic Biology
|
| Street address |
1068, Xueyuan Road
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
518055 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE155186 |
Bromodomain testis-specific protein BRDT directs ΔNp63 function and super enhancer activity in a distinct subset of esophageal squamous cell carcinomas [RNA-seq] |
| GSE155187 |
Bromodomain testis-specific protein BRDT directs ΔNp63 function and super enhancer activity in a distinct subset of esophageal squamous cell carcinomas |
|
| Relations |
| BioSample |
SAMN15651068 |
| SRA |
SRX8831827 |
