|
| Status |
Public on May 02, 2019 |
| Title |
U87 empty vector_2 |
| Sample type |
SRA |
| |
|
| Source name |
U87 MG glioblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87
treatment: Control
|
| Treatment protocol |
Total RNA was isolated from U87 cells expressing either empty vector or ERβ expression vector and subjected to RNA-seq analysis
|
| Growth protocol |
U87 cells were cultured in DMEM media supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
U87 cells transduced with lentiviral particles carrying either empty vector or ERβ FLAG expression vector and total RNA was isolated using RNeasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
U87 cells expressing empty vector
|
| Data processing |
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
Oct 16, 2018 |
| Last update date |
May 02, 2019 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
|
| Organization name |
UTHSA-GCCRI
|
| Street address |
8403 Floyd Curl Drive
|
| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE121332 |
Estrogen receptor beta enhances chemotherapy response of GBM cells by down regulating DNA damage response pathways |
|
| Relations |
| BioSample |
SAMN10247380 |
| SRA |
SRX4893186 |
