|
| Status |
Public on Mar 02, 2016 |
| Title |
BCPAP-Prx_PBS |
| Sample type |
SRA |
| |
|
| Source name |
PBS-treated control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BCPAP
cell type: Thyroid cancer
|
| Treatment protocol |
Doxycyclin (0.5 µg/ml) or PBS was treated for 48 hours
|
| Growth protocol |
The cells were grown in standad culture media (DMEM containing 10% Fetal Bovine Serum and antibiotics)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected directly into Trizol lysis buffer (Sigma-Aldrich) and total RNA was immediately extracted following the manufacturer’s protocol. Total RNAs were dissolved in H2O and quantified on a NanoDrop 2000 spectrophotometer (NanoDrop Products, Wilmington, DE, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw data files in FASTQ format was analyzed with Illumina BaseSpace
TopHat algorithm was used to align the raw reads to human hg19 genome assembly
Cufflinks was used to quantify the aligned reads and to analyze differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited gene.fpkm_tracking files include FPKM values generated by the Cufflinks algorithm
|
| |
|
| Submission date |
Nov 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Young-Kwon Hong |
| Organization name |
University of Southern California
|
| Street address |
1450 Biggy St. NRT6501
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE75059 |
Transcriptional profile changes by Prox1 expression in thyroid cancer cells |
|
| Relations |
| BioSample |
SAMN04271423 |
| SRA |
SRX1433732 |
