|
| Status |
Public on Sep 18, 2017 |
| Title |
F19_pvll |
| Sample type |
SRA |
| |
|
| Source name |
VMHpvll
|
| Organism |
Mus musculus |
| Characteristics |
background: VgluT2-cre/Ai6
Sex: female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
coronal frozen sections of VgluT2-cre/Ai6 female mice. VMHpvlm and VMHpvll were microdissected using LCM. RNA extracted using picopure (ThermoFisher).
Clontech SMARTer Stranded Total RNA-Seq Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The RNA-seq libraries were then prepared using Clontech SMARTer Stranded Total RNA-Seq Kit (cat. no. 635006) and purified using AMPure beads (Beckman Coulter). The quantity of the library was examined using Qubit RNA HS assay Kit (Thermo Fisher Scientific) and qPCR. The quality of the library was determined using Bioanalyzer (Agilent). Once the libraries were deemed high quality (free of adaptor dimers and in concentration >2 nM), we pooled eight samples equimolarly and sequenced them by Illumina HiSeq 2500 using high output mode to achieve greater depth of coverage. Read alignment was carried out using HISAT2 (https://github.com/infphilo/hisat2) against the mouse mm10 reference genome obtained from Ensembl database (http://ensembl.org/)[
The alignment results were then exported to the open-source software Featurecounts to determine the number of reads for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts per gene per sample
|
| |
|
| Submission date |
Aug 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Koichi Hashikawa |
| E-mail(s) |
lifeasadolphin@gmail.com
|
| Phone |
6463186592
|
| Organization name |
University of Washington
|
| Department |
Neuroscience
|
| Lab |
Stuber
|
| Street address |
1959 NE Pacific St. HSB J135
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE103183 |
Transcriptional profiles of female VMHpvlm and VMHpvll |
|
| Relations |
| BioSample |
SAMN07568525 |
| SRA |
SRX3141575 |
