|
| Status |
Public on Oct 12, 2015 |
| Title |
LHSAR_FOXA1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
LHSAR_FOXA1_rep2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LHSAR
cell type: LHSAR overexpressed with FOXA1
treatment: 1nM R1881
|
| Treatment protocol |
Cells were plated 1 day prior to infection with appropriate lentivirus and medium was replaced 24 hours later with medium with R1881. Cells were harvested 48 hours after addition of R1881.
|
| Growth protocol |
Cells were grown in PrEGM medium. Cells were passaged every 3-4 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction was performed using a Qiagen RNA preparation kit per standard protocol
Libraries were constructed using purified total RNA as above. Polyadenylated mRNA was purified, and the library for RNAseq was constructed using the Truseq v2 kit (Illumina). Quality control was assessed by BioA analysis (Agilent Technologies) prior to library construction and again prior to sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequence reads were aligned to the hg19 genome using STAR
Gene expression levels were called using Cufflinks
Differential expressed genes were called using LIMMA
Genome_build: hg19
Supplementary_files_format_and_content: FPKM expression level table
|
| |
|
| Submission date |
Jun 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Fugen Li |
| E-mail(s) |
fugen_li@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE70078 |
Androgen receptor programming in human tissue implicates HOXB13 in prostate pathogenesis [RNA-Seq] |
| GSE70079 |
Androgen receptor programming in human tissue implicates HOXB13 in prostate pathogenesis |
|
| Relations |
| BioSample |
SAMN03783413 |
| SRA |
SRX1067098 |
