|
Status |
Public on Feb 11, 2017 |
Title |
shRUNX2_3_repeat3 |
Sample type |
SRA |
|
|
Source name |
SAOS2 cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: SAOS2 tissue: cell culture passage: less than 30 passages drug resistance: puromycin selection for 6 days after lentiviral transduction
|
Growth protocol |
SAOS2 were grown in DMEM, 10% Fetal Bovine Serum, and 1X penicillin-streptomycin (All from Invitrogen).
|
Extracted molecule |
total RNA |
Extraction protocol |
RNAs were extracted using the GenElute Mammalian total RNA Miniprep kit (Sigma, Cat: RTN350-1kt). Illumina TruSeq RNA, Protocol RS-930-2001 with Illumina TruSeq V3.0
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
RNA with Poly A tail
|
Data processing |
Base calling: RTA 1.12.4.2 (performed at the Next Generation Sequencing Facility at the Center for Cancer Research at the National Cancer Institute) Demultiplexing: Casava 1.8.2 allowing 1 mismatch Alignment and filtering: tophat -G hg19_Ensemble_v70.gtf -o ./ -r 10 --mate-std-dev 200 -p 16 read1.fastq read2.fastq To generate FPKM files: Cufflinks using a gtf file of hg19 (Refseq) downloaded on 08/24/2014 from UCSC browser. Genome_build: hg19 Supplementary_files_format_and_content: FPKM files were generated using Cufflinks
|
|
|
Submission date |
Jan 28, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Jing Huang |
E-mail(s) |
huangj3@mail.nih.gov
|
Organization name |
National Cancer Institute
|
Lab |
Cancer Biology and Genetics
|
Street address |
37 Convent Dr. 37/3140
|
City |
Bethesda |
State/province |
MD |
ZIP/Postal code |
MD 20892 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE77352 |
A RUNX2-mediated Epigenetic Regulation of the Survival of p53 Defective Cancer Cells |
|
Relations |
BioSample |
SAMN04446414 |
SRA |
SRX1551010 |