|
| Status |
Public on Mar 12, 2018 |
| Title |
ROM2 |
| Sample type |
SRA |
| |
|
| Source name |
Shank3-deficient_romidepsin
|
| Organism |
Mus musculus |
| Characteristics |
age: Young; 5-6 weeks old
genotype/variation: Shank3-deficient
treated with: romidepsin (0.25 mg/kg, i.p., once daily for 3 days)
tissue: prefrontal cortical slices
cell type: neurons
|
| Treatment protocol |
Young mice (5-6 weeks old) were treated with saline or romidepsin (0.25 mg/kg, i.p., once daily for 3 days). Animals were sacrificed 1 day later after the last treatment for tissue collection.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA Extraction with TRIZOL Reagent and Purification with QIAGEN. RNeasy Mini Kit(cat # 74104).
cDNA libraries were prepared using the TrueSeq RNA Sample Preparation Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling was performed with bcl2fastq version 2.17.1.14
Mapping to genome with TopHat (v2.1.1) with default parameters
Expression level was quantified as Read Count using htseq-count (HTSeq/0.6.1) and genes.gtf (mm10)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include Read Count value for each sample
|
| |
|
| Submission date |
Jan 17, 2018 |
| Last update date |
Mar 12, 2018 |
| Contact name |
Zhen Yan |
| E-mail(s) |
zhenyan@buffalo.edu
|
| Phone |
(716) 829-3058
|
| Organization name |
University at Buffalo
|
| Department |
Physiology and Biophysics
|
| Street address |
124 Sherman Hall
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14214 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE109328 |
Epigenetic Rescue of Autism-like Social Deficits in Shank3-Deficient Mouse Models |
|
| Relations |
| BioSample |
SAMN08373051 |
| SRA |
SRX3589912 |
