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Sample GSM1682834 Query DataSets for GSM1682834
Status Public on Mar 09, 2018
Title TC32 Etop_6
Sample type SRA
 
Source name Ewing's sarcoma TC32
Organism Homo sapiens
Characteristics cell line: TC32
cell type: Ewing's sarcoma
growth protocol: Cells were grown in RPMI-40 supplemented with 10%FBS
treatment prototcol: 0.05μM Etoposide for 6 hours
Treatment protocol Samples were treated with either vehicle (DMSO) or indicated doses of etoposide for indicated amout of time before extraction of RNA
Growth protocol Cells were passaged in 10cm corningware dishes using media described in Samples section in a 37°C humidified incubator
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from sub-confluent 10cm dishes using Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
 
Submission date May 13, 2015
Last update date May 15, 2019
Contact name Yidong Chen
E-mail(s) cheny8@uthscsa.edu
Phone 2105629163
Organization name UT Health Science Center at San Antonio
Department Population Health Sciences
Street address 8403 Floyd Curl Drive, MSC 7784
City San Antonio
State/province Texas
ZIP/Postal code 78229
Country USA
 
Platform ID GPL11154
Series (2)
GSE68836 BRCA1, R-loops and Recombination defects in Ewing's sarcoma (RNA-seq)
GSE68847 BRCA1, R-loops and Recombination defects in Ewing's sarcoma
Relations
BioSample SAMN03656606
SRA SRX1025861

Supplementary file Size Download File type/resource
GSM1682834_Sample_TC32_Etop_6_Genes_ReadCount.txt.gz 96.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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