|
| Status |
Public on Nov 02, 2022 |
| Title |
NA_KCl_6h_rep2_RNA_seq |
| Sample type |
SRA |
| |
|
| Source name |
E16.5 mouse cortical neurons
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
kcl treatment: 6 h
developmental stage: E16.5
tissue/cell type: E16.5 mouse cortical neurons
genotype: WT
gender: pooled male and female
|
| Treatment protocol |
At DIV6, neuronal cells were silenced with 1 μM tetrodotoxin (TTX; Fisher) and 100 μM DL-2-amino-5-phosphopentanoic acid (DL-AP5; Fisher) overnight. The next morning, neuronal cells were depolarized with 55mM KCl for 0h, 2h, and 6h. At the end time point, the neuronal cells were harvested for RNA extraction.
|
| Growth protocol |
E16.5 mouse cortex tissues were dissected and dissociated into single cell suspension, resuspended in neuronal culture media (Neurobasal medium containing 2% B27 supplement (Invitrogen), 1% Glutamax (ThermoFisher) and 1% penicillin-streptomycin (ThermoFisher)) and seeded on laminin and poly-ornithine coated 10-cm dishes. Neurons were grown in vitro for 7 days with fresh medium changed on DIV3 and DIV6.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from the neuronal cultures using TRIzol reagent combined with RNeasy min kit (QIAGEN) with DNase I on-column digestion.
Two rounds of poly(A) selection was performed and RNA-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Fastp v0.20 was used to remove adapter sequences, identify and remove low-quality reads and called bases.
After trimming, reads with length longer than 30nt were mapped to mm10 by RSEM (v1.3.0) with Bowtie2 (v2.2.9).
Assembly: mm10
Supplementary files format and content: tab-delimited files containing transcript abundance counts
|
| |
|
| Submission date |
Apr 26, 2022 |
| Last update date |
Nov 02, 2022 |
| Contact name |
Xiguang Xu |
| E-mail(s) |
xiguang@vt.edu
|
| Organization name |
Virginia Tech
|
| Department |
Department of Biomedical Sciences and Pathobiology
|
| Lab |
Epigenomics and Computational Biology Laboratory
|
| Street address |
1015 Life Science Circle
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24060 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE201636 |
RNA-seq of E16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h. |
| GSE201637 |
RNA bisulfite sequencing and RNA-seq of 16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h |
|
| Relations |
| BioSample |
SAMN27861745 |
| SRA |
SRX15010761 |
