|
| Status |
Public on Apr 24, 2020 |
| Title |
U87_ control siRNA_1 |
| Sample type |
SRA |
| |
|
| Source name |
U87 MG glioblastoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U87
sirna: Control
|
| Treatment protocol |
Total RNA was isolated from U87 cells transfected with control siRNA or PELP1 siRNA 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 transfected with control siRNA or PELP1 siRNA using oligofectamine transfection reagent and after 72 hours 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 transfected with control siRNA.
|
| 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 (GRCh37)
Supplementary_files_format_and_content: *_Genes_ReadCount.txt: 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 |
May 20, 2019 |
| Last update date |
Apr 24, 2020 |
| 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) |
| GSE131502 |
Proline Glutamic acid and Leucine rich Protein 1 (PELP1) promotes glioblastoma progression by enhancing Wnt/β-catenin signaling |
|
| Relations |
| BioSample |
SAMN11785369 |
| SRA |
SRX5867742 |
