|
| Status |
Public on Jan 27, 2016 |
| Title |
AMY_KO_2_783 |
| Sample type |
SRA |
| |
|
| Source name |
Adult Amygdala
|
| Organism |
Mus musculus |
| Characteristics |
genotype: SMCX KO
gender: male
tissue type: Adult Amygdala
|
| Treatment protocol |
KCl Treated' cortical neurons were treated with 50mM KCl for 60 minutes.
|
| Growth protocol |
Cortices from E16.5 male mouse embryos were collected in HHGN dissection solution (Hanks' Balanced Salt Solution supplemented with 2.5 mM Hepes, 35 mM Glucose, 4 mM sodium bicarbonate). Cortices were incubated with 0.1% trypsin (Life Technologies) in HHGN for 20 min. at room temperature, quenched in Neurobasal media (Life Technologies) containing 10% fetal bovine serum (FBS), and triturated in Neurobasal media containing 0.01 mg/ml DNaseI. Dissociated cells were suspended in Neurobasal media supplemented with 1x B27 solution (Life Technologies), 1x penicillin-streptomycin , 0.5 mM L-glutamine, and 25 mM 2-mercaptoethanol. Cells from one cortex were plated in a 10-cm tissue culture dish treated with 50 mg/ml Poly-D-lysine hydrobromide (Sigma, MW 30,000-70,000). Cultured are maintained in humidified incubators with 5% CO2 at 37°C. Half of culture media was replaced with new culture media every 3 days in vitro (DIV), and cells were harvested on 9 or 10 DIV.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified through Purelink RNA Mini Kit (Life Technologies). rRNA was depleted using RiboMinus Eukaryote kit for RNA-Seq (Life Technologies).
RNA-Seq libraries were prepared by Direct Ligation of Adapters to First Strand cDNA (DLAF) where splinted adapters were ligated to single-stranded first strand cDNA. The novel method is described in a manuscript under revision and the reference will be updated soon.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
AMY_KO_2_783_S8_L002_R1_001
|
| Data processing |
Following sequencing cluster imaging, base calling were conducted using the Illumina pipeline.
RNA-Seq reads were mapped to mm9 build using TOPHAT v2.1.1 and Bowtie 2 allowing for upto 2 mismatches.
Aligned BAM files were normalized to the sequencing depth and converted to bigwig files in a strand-specific manner using bedtobedgraph and wigtobigwig utilities.
Genome_build: mm9
|
| |
|
| Submission date |
Nov 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Saurabh Agarwal |
| E-mail(s) |
saurabha@umich.edu
|
| Phone |
7346478811
|
| Organization name |
University of Michigan
|
| Department |
Human Genetics
|
| Lab |
Shigeki Iwase
|
| Street address |
1241 E. Catherine St. 5815 Medical Science II
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE61036 |
Aggression, cognitive and neurodevelopmental abnormalities associated with disruption of the intellectual disability and histone demethylase gene Kdm5c |
| GSE74630 |
RNA-Seq of Pre-frontal cortex (PFC) and Amygdala from 3-6 month old adult mice |
|
| Relations |
| BioSample |
SAMN04231539 |
| SRA |
SRX1410903 |
