|
| Status |
Public on Oct 26, 2016 |
| Title |
RNA-seq siRNA control rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Human prostate cancer cell line C42B
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: C42B
transfection: control (D0018101005)
|
| Treatment protocol |
For transient knockdown, C4-2B cells were transfected with 100nM of siRNA oligonucleotides of human HOXC6 (L011871000005), DLX1 (L011871000005), ZFP41 (L018062020005) or control (D0018101005) using SMART pool Dharmafect transfection reagent 3 (Dharmacon, Lafayette, CO) for 72 h.
|
| Growth protocol |
C42B cells were grown in RPMI 1640 supplemented with 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, RNA was extracted using Trizol reagent (15596-026) (Life technologies, Carlsbad, CA) following its protocol.
RNA-seq libraries were made using KAPA Stranded mRNA-Seq Kit with KAPA mRNA Capture Beads (KK8420) (Kapa Biosystems, Woburn, MA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
RNA-seq reads were aligned to hg19 genome assembly using Tophat2 after trimming raw reads, quality score <20 in Partek Flow version 3.
For RNA-seq, GENCODE v19 was used to quantify to transcriptome.
For RNA-seq, differentially expressed genes analyzed by using the Gene Specific Algorithm (Upper Quartile normalization) from Partek Flow version 3.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tab-delimited text files include normalized Upper Quartile for each gene.
|
| |
|
| Submission date |
Mar 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Suhn K Rhie |
| Organization name |
University of Southern California
|
| Street address |
1450 Biggy Street
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE78913 |
Tracing Enhancer Networks using Epigenetic Traits (TENET) |
|
| Relations |
| BioSample |
SAMN04532537 |
| SRA |
SRX1613564 |
