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Sample GSM2214061 Query DataSets for GSM2214061
Status Public on Apr 27, 2017
Title 7250-empty RNA-seq
Sample type SRA
Source name Fibroblast cell line, empty vector added
Organism Homo sapiens
Characteristics cell line: 7250
cell type: fibroblast
treatment time: NA
treatment: NA
Treatment protocol Drug was dissolved in DMSO to a stock conentration of 10 mM, and additionally diluted in DMEM to a final concentration of 500 nM (or DMSO of equivilent final volume), exposing cells for 6 hours before extracting RNA. For shRNA inducible experiments, cells were treated for 48 hours with doxycyclin (100 ng/mL).
Growth protocol Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.
Extracted molecule total RNA
Extraction protocol RNA was extracted from RMS cell lines, RH4 and RH41 treated with DMSO or JQ1 for 6 hours, or inducible shRNA derived RH4 cells, using the RNeasy mini kit (Qiagen).
Standard Illumina barcodes were introduced during library preparation
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing RNA-seq reads were aligned to the hg19 reference genome using TopHat.
Gene expression values were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks and the UCSC reference at the gene level.
Differential gene expression was determined using Cuffdiff (
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM files are provided in txt format at the gene-level
Submission date Jun 26, 2016
Last update date May 15, 2019
Contact name Javed Khan
Phone 2407606135
Organization name NCI, NIH
Department Genetics Branch
Lab Javed Khan
Street address 37 Convent Dr.
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL11154
Series (2)
GSE83724 PAX3-FOXO1 requires BRD4 to drive oncogene addiction in RMS cells [RNA-seq]
GSE83728 Epigenetic Lanscape and BRD4 Transcriptional Dependency of PAX3-FOXO1 Driven Rhabdomyosarcoma
BioSample SAMN05293625
SRA SRX1878927

Supplementary file Size Download File type/resource
GSM2214061_Sample_LNCXNILC_T_D26GWACXX.genes.fpkm_tracking.gz 792.7 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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