|
| Status |
Public on Feb 20, 2021 |
| Title |
Ctrl_A |
| Sample type |
SRA |
| |
|
| Source name |
Ctrl_neurons
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
age: DIV 15
tissue: Hippocampus
cell type: Cultured rat hippocampal neurons
treated with: mock-cLTP solution
|
| Treatment protocol |
Ctrl samples were treated with mock-cLTP solution. Others were treated with cLTP solution.
|
| Growth protocol |
Neurons were cultured with Neurobasal medium supplemented with SM1 and maintained at 37 °C in a humidified 5% CO2 atmosphere incubator. Cultures were fed three time a week.Glial growth was suppressed by the addition of 5-fluoro-2-deoxyuridine (20 mg/ml; Sigma-Aldrich) and uridine (20 mg/ml; Sigma-Aldrich) at day 4 after plating (DIV4).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from neurons using RNeasy mini Kit (Qiagen). Ribosomal RNA was depleted with RiboZero kit (Epicenter). (Thermo).
Poly(A)-enriched RNA were separated by 3 rounds of Oligo(dT) magnetic beads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
mock-cLTP treatment, biological repeat 1
|
| Data processing |
Bases were called with Illumina's bcl2fastq software program.
Reads were trimmed for low quality (<30) 3' sequence to a minimum read length of 20 bp.
Reads were aligned to rat genome assembly rn6 using Tophat v2.1.0 and the Ensembl84 reference transcriptome.
Gene counts were quantified from BAM files using htseq-counts and the Ensembl84 reference transcriptome.
Differentially expressed genes were identified pairwise between each time point and mock control, using the R package edgeR.
Genome_build: RN6
Supplementary_files_format_and_content: Excel file with results compiled from all four pairwise comparisons (treatment vs control).
|
| |
|
| Submission date |
Feb 20, 2018 |
| Last update date |
Feb 20, 2021 |
| Contact name |
Elizabeth Thomas Bartom |
| E-mail(s) |
ebartom@northwestern.edu
|
| Organization name |
NORTHWESTERN UNIVERSITY AT CHICAGO
|
| Department |
Biochemistry and Molecular Genetics
|
| Lab |
Bartom
|
| Street address |
303 E Superior Ave, SQBRC 7-406
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE110908 |
RNA Sequencing quantitatively profiles chemical long-term potentiation (LTP) induced gene transcription alteration |
|
| Relations |
| BioSample |
SAMN08574187 |
| SRA |
SRX3729442 |
