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Sample GSM1163687 Query DataSets for GSM1163687
Status Public on Jun 15, 2013
Title Selected AHR DIFFD5 PURO Rep 2
Sample type SRA
 
Source name Embryonic Stem Cells
Organism Mus musculus
Characteristics strain: C57BL/6J
cell group: Selected AHR+ Cells
treatment: Ctrl
day: 5
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1000
 
Description Selected AHR DIFFD5 PURO Rep 2
Data processing bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns
 
Submission date Jun 14, 2013
Last update date May 15, 2019
Contact name Mario Medvedovic
Organization name University of Cincinnati
Department Department of Environmental Health
Lab Laboratory for Statistical Genomics and Systems Biology
Street address 3223 Eden Av. ML 56
City Cincinnati
State/province OH
ZIP/Postal code 45267-0056
Country USA
 
Platform ID GPL15103
Series (1)
GSE47964 Activation of the aryl hydrocarbon receptor by dioxin during embryonic stem cell differentiation disrupts the expression of homeobox transcription factors that control cardiomyogenesis
Relations
BioSample SAMN02204145
SRA SRX306234

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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