|
| Status |
Public on Jul 26, 2018 |
| Title |
KO3_brain_2 |
| Sample type |
SRA |
| |
|
| Source name |
KO3_brain_2
|
| Organism |
Macaca fascicularis |
| Characteristics |
Stage: Newborn
tissue: brain
genotype: SIRT6 mutant
|
| Treatment protocol |
Monkey tissues were homogenized in liquid nitrogen, then RNA were extracted using TRIzol reagent protocol, and purified using RNeasy Mini Kit (Qiagen) according to the manuals. After quantification of RNA by Fragment Analyzer (Advanced Analytical), 1.5 μg of total RNA was used to construct sequencing libraries by TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer’s standard protocol. The libraries were sequenced on the HiSeq X Ten platform.
|
| Growth protocol |
The tissue samples of cynomolgus monkeys (Macaca fascicularis)at a gestation period of 2, 4 month of embryonic monkey and newborn stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
FPKM_tissue.txt
|
| Data processing |
Basecalls performed by Casava using default settings
The clean reads were mapped to the macFas5 genome and assembled using HISAT, version 0.1.6-beta.
Each read with a unique genomic location in the bam format was retained for a gene expression calculation using Cufflinks (version 2.0.2) with the option “--GTF”.
The gene annotation was downloaded from NCBI (GCF_000364345.1), and only exon annotation for mRNA and other ncRNAs were used .
Genes with at least 1 FPKM (Fragments Per Kilobase of exon per Million fragments mapped) in at least one sample were used for the differentially expressed gene analyses
Genome_build: macFas5
Supplementary_files_format_and_content: FPKM files estimated by Cufflinks
|
| |
|
| Submission date |
Aug 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Qi Zhou |
| E-mail(s) |
zhouqi@ioz.ac.cn
|
| Organization name |
Institute of Zoology,CAS
|
| Lab |
Zhou
|
| Street address |
Datun Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL23096 |
| Series (1) |
| GSE102830 |
Deficiency of SIRT6 results in developmental retardation in cynomolgus monkeys |
|
| Relations |
| BioSample |
SAMN07520095 |
| SRA |
SRX3104149 |
