|
| Status |
Public on May 18, 2021 |
| Title |
Neuron wildtype, Basal --littermate control for Brg1-SA samples, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Neuron
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild-type
cell type: primary cortical neurons
treatment: Basal level of KCl
|
| Treatment protocol |
For depolarization, the cultures were pretreated with TTX (1 µM) and APV (100 µM) to inhibit spontaneous activation on 5 div and 50 mM KCl was added to the cultures for 1 h on 6 div.
|
| Growth protocol |
Primary cortical neurons were culture from E16.5 mouse embryo. Dissociated cortical neurons were plated on poly-L-ornithine- and fibronectin-coated wells. Culture media contained neurobasal plus with B27 plus supplement (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were expreact with TRIZOL and cleaned with a Qiagen RNeasy Kit.
RNA-seq libraries were prepared using the Illumina RNA-Seq Preparation Kit and sequenced at the University of Texas Southwestern Sequencing Core Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
WT_SA1_con
|
| Data processing |
Kallisto (version 0.43.1) was used to quantify gene expression with GENCODE annotation M15 for GRCm38.
The parameter used in Kallisto is "--bias"
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The columns in Kallisto output are isoform_id, length, effective-length, estimated_read_count, TPM.
|
| |
|
| Submission date |
May 17, 2021 |
| Last update date |
May 18, 2021 |
| Contact name |
Zhenyu Xuan |
| E-mail(s) |
zhenyu.xuan@utdallas.edu
|
| Phone |
972-883-2518
|
| Organization name |
UT Dallas
|
| Street address |
800 West Campbell
|
| City |
Richardson |
| State/province |
TX |
| ZIP/Postal code |
75080 |
| Country |
USA |
| |
|
| Platform ID |
GPL28457 |
| Series (2) |
| GSE174584 |
BRG1 S1382 phosphorylation regulates neuronal activity-dependent gene activation [RNA-seq_B] |
| GSE174585 |
BRG1 role in neuronal activity |
|
| Relations |
| BioSample |
SAMN19235177 |
| SRA |
SRX10913963 |
