|
| Status |
Public on Nov 01, 2014 |
| Title |
A673 shGFP-2 |
| Sample type |
SRA |
| |
|
| Source name |
A673 Ewing cells expressing control shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A673
cell type: Ewing's sarcoma
|
| Treatment protocol |
Cells were infected with lenti-virus containing shRNA either for GFP or hnRNPK and selected with puromycin.
|
| Growth protocol |
Cells were grown in DMEM supplemented with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
5 days post infection, RNA was extracted using TRIzol.
NuGen Encore Complete kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
STAR 2.3.0 cufflinks 2.1.1
Sequenced reads were mapped to hg19 whole genome using STAR aligner.Genome generation is from iGenomes
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks 2.1.1 software
Genome_build: hg19
Supplementary_files_format_and_content: FPKM tracking file with FPKM for each sample
|
| |
|
| Submission date |
Aug 28, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Dedeepya Vaka |
| E-mail(s) |
dvaka@stanford.edu
|
| Organization name |
Stanford
|
| Department |
Pediatrics
|
| Lab |
Alejandro Sweet-Cordero
|
| Street address |
265 Campus Drive
|
| City |
Palo Alto |
| ZIP/Postal code |
94035 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE60890 |
hnRNPK knock down in Ewing cell line |
| GSE60891 |
The long non-coding RNA lnc277 mediates a repressive gene signature in Ewing's sarcoma and is required for oncogenesis |
|
| Relations |
| BioSample |
SAMN03012767 |
| SRA |
SRX689284 |
