|
| Status |
Public on Dec 17, 2017 |
| Title |
P14-DH-2 |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal hippocampus from P14
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Dorsal hippocampal tissue
age: Dorsal hippocampus from P14 brain
strain: Sprague-Dawley
|
| 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 sequencing library was prepared using the Illumina TruSeqStranded mRNA Sample Preparation Kits (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 NextSeq 500 |
| |
|
| Data processing |
Paired-end sequencing (150 x 2) was performed using a Nextseq-500 (Illumina).
Reference genome sequence data from Homo sapiens were obtained from the University of California Santa Cruz Genome Browser Gateway (assembly ID: rn5). 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 17,070 RefSeq (UCSC rn5) 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. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Mar 10, 2017 |
| 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) |
| GSE96079 |
Transcriptome-based analysis of developing dorsal and ventral hippocampus |
|
| Relations |
| BioSample |
SAMN06561724 |
| SRA |
SRX2633268 |
