|
| Status |
Public on Apr 04, 2024 |
| Title |
Hippocampus, PBS treatment, Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
brain region hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain region hippocampus
treatment: PBS
|
| Treatment protocol |
Mice were injected subcutanuously with EU (50 mg/kg) or PBS (equal volume) at postnatal days P3-P5 (one injection daily). Hippocampus tissue was dissected from the brain on postnatal day P36.
|
| Growth protocol |
Mice housed in 12:12 light:dark cycle under SPF conditions and given ad libitum access to mouse chow and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using miRNeasy Kit with gDNA removal columns. EU-labelled RNA was purified using Biotin-Click reaction and Streptavidin beads. PBS-treated samples underwent the same extraction protocol.
Libraries were prepared using Universal Plus Total RNA-seq kit (TECAN).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fragments were demultiplexed using bcl2fastq2 (v2.20.0) and aligned to the mouse reference GRCm39 with the support of Ensembl gene annotation version 104 using the STAR (v2.7.10b) aligner. Fragments per gene and samples were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl gene annotation using featureCounts (v2.0.1).
Assembly: GRCm39
Supplementary files format and content: Tab separated Excel Table from featureCounts. The rows are genes and the columns provide gene information and list of samples.
|
| |
|
| Submission date |
Nov 17, 2023 |
| Last update date |
Apr 04, 2024 |
| Contact name |
Tomohisa Toda |
| E-mail(s) |
tomohisa.toda@fau.de
|
| Organization name |
DZNE
|
| Street address |
Tatzberg 41
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE248100 |
Life-long persistence of nuclear RNAs in the mouse brain [Hippocampus] |
| GSE248101 |
Life-long persistence of nuclear RNAs in the mouse brain |
|
| Relations |
| BioSample |
SAMN38300118 |
| SRA |
SRX22558572 |
