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Sample GSM1622376 Query DataSets for GSM1622376
Status Public on Dec 09, 2015
Title Female dexamethasone treatment, biological replicate 1
Sample type SRA
Source name Female dexamethasone treatment, biological replicate 1
Organism Mus musculus
Characteristics strain: C57Bl/6
age: embryonic day E14.5
gender: Female
treatment: Dexamethasone
Treatment protocol Neurospheres at third passage were treated with 100 nM dexamethasone or equivalent volumes of ethanol vehicle for 4 hours
Growth protocol Hypothalamus dissected from embryonic day 14.5 fetal mice were dissociated into single cells and then cultured as neurospheres
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
The Ilumina Stranded Total RNA-Seq Kit was used to construct the library per manufactuer's instructions
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description Sample G
Data processing Sequenced reads are mapped to Ensembl GRCm38 reference genome using Tophat2 v2.0.9 (default parameters)
The transcripts are assembled using Cufflinks v2.2.1 (default parameters)
The replicates assemblies are merged with the reference transcriptome annotation using Cuffmerge v.2.2.1 (default parameters).
Cuffdiff v2.2.1 (default parameters) is then used to calculate the expression levels and perform differential expression analysis using the merged assembly and the mapped reads.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample as produced by Cuffdiff
Submission date Mar 02, 2015
Last update date May 15, 2019
Contact name Uma Chandran
Phone 412-648-9326
Organization name University of Pittsburgh
Department BioMedical Informatics
Street address 5150 Center Ave
City Pittsburgh
State/province PA
ZIP/Postal code 15232
Country USA
Platform ID GPL17021
Series (1)
GSE55113 Expression data from dexamethasone treated mouse embryonic hypothalamic progenitor/stem cells isolated from wild type C57Bl/6 male or female mice
BioSample SAMN03381414
SRA SRX1463155

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

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