|
| Status |
Public on Mar 20, 2023 |
| Title |
OL_KO_HC-2 |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus from Ccnyknockout mouse after Morris water maze original learning
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse Hippocampal tissue
age: 8-10 weeks old
strain: C57BL/6J
|
| Treatment protocol |
Morris water maze original and reversal learning tasks were applied to wild-type and Ccny knockout mice. All experimental protocols were approved by the KIST Institutional Animal Care and Use Committee (approval number 2018-048)
|
| Growth protocol |
Mice were bred and maintained at the SPF facility in the Korea Institute of Science and Technology (KIST).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the hippocampal tissues using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Paired-end sequencing (101 x 2) was performed using a Hiseq (Illumina).
Illumina Casava1.7 software used for basecalling.
mapped to mm10 whole genome using STAR v2.5.1.
Gene expression levels were calculated count-per-million (CPM) values normalized with trimmed mean of M-values (TMM) using an edgeR v.3.12.1. The CPM values are on log2 scale.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample
|
| |
|
| Submission date |
Apr 04, 2019 |
| Last update date |
Mar 20, 2023 |
| Contact name |
Jong Hwan Kim |
| E-mail(s) |
kkjjhhk@kribb.re.kr
|
| Phone |
0821093299557
|
| Organization name |
Korea Research Institute of Bioscience and Biotechnology
|
| Department |
Genome structure research center
|
| Street address |
125 Gwahak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
ASI|KR|KS015|DAEJEON |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE129324 |
Transcriptome-based analysis of CCNY-mediated learning and memory in the hippocampus |
|
| Relations |
| BioSample |
SAMN11340194 |
| SRA |
SRX5635831 |
