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Sample GSM2214066 Query DataSets for GSM2214066
Status Public on Apr 27, 2017
Title RH4 DMSO 6hr RNA-seq
Sample type SRA
 
Source name RMS cell line, PAX3-FOXO1
Organism Homo sapiens
Characteristics cell line: RH4
cell type: rhabdomyosarcoma
treatment time: 6 hours
treatment: DMSO
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 NextSeq 500
 
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 (http://cole-trapnell-lab.github.io/cufflinks/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
E-mail(s) khanjav@mail.nih.gov
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 GPL18573
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
Relations
BioSample SAMN05293630
SRA SRX1878932

Supplementary file Size Download File type/resource
GSM2214066_Sample_Rh4_dmso_6h_rz_T_H3YCHBGXX.genes.fpkm_tracking.gz 810.4 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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