|
| Status |
Public on Jun 16, 2016 |
| Title |
YAP |
| Sample type |
SRA |
| |
|
| Source name |
Lung carcinoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H157
cell type: Lung carcinoma cells
genotype/variation: expressing YAP
|
| Treatment protocol |
The H157 lung carcinoma cells stably expressing different construct were collected after reaching mid-log growth phase, then subject to RNA purification
|
| Growth protocol |
The H157 lung carcinoma cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were purified from cells using Trizol method and subsequently cleaned using RNAeasy Kit.
Total RNA not exceeding 3 μg was further used to purify polyadenylated RNA using Illumina TruSeq Total RNA Sample Prep kits. We used the Ribo-Zero Human to remove cytoplasmic rRNA. The mRNA purified was further analyzed using Bioanalyzer (Agilent Technologies) prior to generation of cDNA library with bar coded ends. RNA-seq libraries were robotically prepared with Illumina TruSeq Total RNA Sample Prep kits according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were aligned to hg19 using Bowtie v2.2.5
The EBSeq tool was used to identify differentially expressed genes in pairwise comparisons of all conditions
Genome_build: hg19
supplementary_files_format_and_content: Gene expression level of all conditions was merged to genes-merge.counts.matrix using rsem-generate-data-matrix. Scores represent expected reads count at each condition derived from rsem-calculate-expression
|
| |
|
| Submission date |
Apr 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Zefeng Wang |
| E-mail(s) |
wangzefeng@picb.ac.cn
|
| Organization name |
CAS-MPG Partner Institute for Computational Biology (PICB)
|
| Street address |
320 Yueyang Road
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE80372 |
A splicing switch of TEAD4 regulates Hippo-YAP signaling pathway to inhibit tumor proliferation |
|
| Relations |
| BioSample |
SAMN04867265 |
| SRA |
SRX1711021 |
