|
| Status |
Public on Oct 22, 2017 |
| Title |
wtEF-3 |
| Sample type |
SRA |
| |
|
| Source name |
wtEF
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A673 cells
RNAi: EWS/FLI
rescue: wt EWS/FLI
batch: 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were trypsinized, counted, and 5 million cells were washed with PBS, pelleted, and flash-frozen. RNA was extracted using an Rneasy kit with on-column DNA digestion per kit instructions (Qiagen). 2.5 ug of total RNA was used for library prep.
Illumina ScriptSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina’s Bcl2fastq conversion software
Sequenced reads were mapped to hg19 whole genome using STAR-2.5.2b using --outSAMunmapped within and otherwise default parameters
Raw counts were generated for each sample using htseq-count with -m intersection-strict -s no -r pos
Normalized counts were generated using default settings and blind = FALSE in the rlog package of DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: csv, Ensembl Gene Accession and normalized count data
|
| |
|
| Submission date |
Feb 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kirsten Johnson |
| E-mail(s) |
kirsten.johnson@nationwidechildrens.org
|
| Phone |
6143552989
|
| Organization name |
Nationwide Childrens Hospital
|
| Department |
Childhood Cancer and Blood Disorders
|
| Lab |
Stephen Lessnick
|
| Street address |
The Research Institute, WA5110, 700 Childrens Drive
|
| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43205 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE94502 |
A novel role for the EWS portion of EWS/FLI in binding GGAA-microsatellites required for oncogenic transformation in Ewing sarcoma [RNA-Seq] |
| GSE94503 |
A novel role for the EWS portion of EWS/FLI in binding GGAA-microsatellites required for oncogenic transformation in Ewing sarcoma |
|
| Relations |
| BioSample |
SAMN06324190 |
| SRA |
SRX2554984 |
