|
| Status |
Public on Jun 01, 2015 |
| Title |
LNCaP-SiGATA2-REP2 |
| Sample type |
SRA |
| |
|
| Source name |
LNCaP-SiGATA2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LNCaP
cell type: prostate cancer cells
treated with: siGATA2
passages: 32-34
|
| Treatment protocol |
4 days before ChIP assay, the full medium was changed to RPMI medium supplied with 5% charcal treated FBS without anti-biotics.
|
| Growth protocol |
LNCaP cells were routinely cutured in RPMI medium supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA mRNA was isolated with Rneasy Mini kit from Qiagen. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample KitPart # 15008136. Briefly, the polyA containing mRNA was purified, fragmented, and reverse transcribed. This was followed by second strand cDNA synthesis. The cDNA fragments went through end repair, adapter ligation, and PCR amplification processes. The final cDNA library was sequenced by Illumina HiSeq2000 in OSUCCC sequencing core.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 4
|
| Data processing |
Sequenced reads were mapped to hg19 by TopHat, and those uniquely mapped reads were used for further analysis.
Differentially expressed genes are retrived by edgeR software with p<0.001.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes differentially expressed gene list from edgeR output
|
| |
|
| Submission date |
Jun 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhenqing Ye |
| E-mail(s) |
yez@uthscsa.edu
|
| Organization name |
The University of Texas Health Science Center at San Antonio
|
| Department |
Department of Molecular Medicine
|
| Street address |
7703 Floyd Curl Drive
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE38393 |
Hi-seq 2000 sequencing facilitates quantitative analysis of transcriptomes in LNCaP cells with or without SiGATA2 treatment. |
| GSE38452 |
A Class of H3K4me1/H3K9me2 marked active GATA2 enhancers directs a GATA2-dependent transcription program underlying prostate cancer progression. |
|
| Relations |
| SRA |
SRX150916 |
| BioSample |
SAMN01001651 |
