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Status |
Public on Mar 20, 2023 |
Title |
OL-RL_WT_HC-3 |
Sample type |
SRA |
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Source name |
Hippocampus from wild-type mouse after Morris water maze original and reversal 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.
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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
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|
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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 |
SAMN11340190 |
SRA |
SRX5635835 |