|
| 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 |
| E-mail(s) |
chandran@pitt.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN03381414 |
| SRA |
SRX1463155 |
