|
| Status |
Public on Feb 10, 2017 |
| Title |
CCNYshRNA_2 |
| Sample type |
SRA |
| |
|
| Source name |
CCNYshRNA, hippocampus from E18 embryos
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
age: E18
cell type: primary culture of hippocampal neurons
genotype/variation: CCNY knockdown
|
| Treatment protocol |
Cultured hippocampal neurons were infected with lentivirus expressing EGFP, CCNY-WT-EGFP or CCNY-shRNA-EGFP at DIV5 or 6.
|
| Growth protocol |
Hippocampal neuron cultures were prepared from E18 Sprague-Dawley (SD) rat embryos and maintained for 14-15 days in vitro (DIV) in Neurobasal media containing B27 supplements.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the infected cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
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.
The sequencing library was prepared using the Illumina TruSeqStranded mRNA Sample Preparation Kits (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HCII_CCNYshRNA_2
|
| Data processing |
Paired-end sequencing (150 x 2) was performed using a Nextseq-500 (Illumina).
Reference genome sequence data from Rattus norvegicus were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: rn4). The reference genome index was built using SAMtools (v. 0.1.19) and the Bowtie2-build component of Bowtie2 (v. 2.1.0). Reads were mapped to the reference genome using Tophat2 (v. 2.0).
The number of fragments per kilobase per million mapped reads (fpkm) for each gene of 17,066 RefSeq (UCSC rn4) gene models was calculated using Cufflinks (v. 2.2.1).
Heat maps were constructed using Mev (v. 4.9.0). Statistical analyses and graph construction were performed using R (v. 3.1.0) and PYTHON (v. 2.7.6).
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.
|
| |
|
| Submission date |
Jul 26, 2016 |
| Last update date |
May 15, 2019 |
| 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 |
GPL20084 |
| Series (1) |
| GSE84850 |
Cyclin Y-mediated changes in RNA-sequencing based transcriptome profiling in hippocampal neurons |
|
| Relations |
| BioSample |
SAMN05440920 |
| SRA |
SRX1977510 |
