|
| Status |
Public on Apr 10, 2018 |
| Title |
U87-ERβ-KO-1 |
| Sample type |
SRA |
| |
|
| Source name |
U87 MG glioblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87 MG glioblastoma
genotype/treatment: ERbeta was knocked out in U87 cells using CRISPR/Cas9 system
|
| Treatment protocol |
Total RNA was isolated from U87 control, U87-ERβ-KO, U87-ERβ1 and U87-ERβ5 cells and subjected to RNAseq analysis
|
| Growth protocol |
U87 cells were cultured in DMEM supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from U87, U87 ERβ-KO, U87 ERβ-KO cells expressing ERβ1 and ERβ5 isoforms using RNeEasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 1-2 µg 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 3000 |
| |
|
| Data processing |
Illumina bcl2fastq 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 |
Sep 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE104296 |
Differential effects of estrogen receptor beta isoforms on glioblastoma progression |
|
| Relations |
| BioSample |
SAMN07703377 |
| SRA |
SRX3218116 |
