|
| Status |
Public on Feb 11, 2017 |
| Title |
shRUNX2_3_repeat1 |
| 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 |
SAMN04446408 |
| SRA |
SRX1551004 |
