|
| Status |
Public on Sep 23, 2016 |
| Title |
MEF2C_WT_3 |
| Sample type |
SRA |
| |
|
| Source name |
Somatosensory Cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed SVeV-129; C57BL/6J
tissue type: Somatosensory Cortex
Sex: M
age: 12 weeks old
genotype/variation: control (Mef2cfl/fl)
|
| Treatment protocol |
RNA was extracted from frozen tissue using Qiagen's Rneasy Kit according to manufacturer's protocol.
|
| Growth protocol |
Mouse regional brain dissections were used and frozen at -80C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
All RNA samples were examined for quantity and quality by NanoDrop and Bioanalyzer. Samples were randomized for RNA extraction and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Protocol 1
|
| Data processing |
Single-end reads were aligned in a staged manner. Reads were aligned with Tophat with Bowtie using default options to a reference sequence comprised of mitochondrial DNA (mm9 from UCSC).
RNA-seq Counts values were quantified using HTSeq python suite, providing gene definitions (mm9 GTF from UCSC).
RNA-seq RPKM values were then quantified using R based on the mm9 GTF annotation from UCSC.
Gene-level RPKMs and Counts quantifications were used for all downstream processing.
Genome_build: Mouse mm9
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample.
|
| |
|
| Submission date |
Sep 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christopher W Cowan |
| E-mail(s) |
cowanc@musc.edu
|
| Phone |
8437922935
|
| Organization name |
Medical University of South Carolina
|
| Department |
Neurosiences; Psychiatry
|
| Street address |
173 Ashley Ave, BSB 403
|
| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
29425 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE87202 |
MEF2C regulates cortical inhibitory and excitatory synapses and behaviors relevant to neurodevelopmental disorders |
|
| Relations |
| BioSample |
SAMN05804808 |
| SRA |
SRX2184916 |
