|
| Status |
Public on Jul 31, 2018 |
| Title |
RNA-Seq of Treeshrew ZIKV-infected PBMC +2dpi, 1 |
| Sample type |
SRA |
| |
|
| Source name |
#1 treeshrew
|
| Organism |
Tupaia chinensis |
| Characteristics |
cell type: PBMC
culture: in vivo
agent: ZIKV
|
| Treatment protocol |
Two treeshreews (duplicated) infected with10^5 PFU of ZIKV(GZ01 strain) by the subcutaneous (s.c.) route.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Peripheral blood mononuclear cells (PBMCs) from 0, 2 and 6 dpi (two for each group) were isolated using Ficoll-Hypaque and total RNA were extracted by RNeasy mini kit (Qiagen, German) for global transcriptome analysis.
RNA libraries were constructed using a TruSeq Stranded mRNA Sample Prep Kit (RS-122-2001, Illumina) according to the manufacturer’s guideline.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
plus2DPBMC-1
|
| Data processing |
bcl2fastq(v 2.17) software was used to base-calling
trimmomatic was used to remove illumina sequencing adapters within raw reads of every sample, trim low quality bases of both read ends
clean reads were mapped to Chinese_treeshrew_KIZv2.gtf by using HISAT (v2.0.4 ), reference genome could be downloaded in website http://www.treeshrewdb.org/
DESeq2 was used to identify DEGs (p<=0.05, FC>=2) based on raw reads counts.
Genome_build: treeshrewdb
Supplementary_files_format_and_content: xls files include reads counts for each Sample
|
| |
|
| Submission date |
May 30, 2018 |
| Last update date |
Jul 31, 2018 |
| Contact name |
feng ma |
| Organization name |
CAMS
|
| Department |
Suzhou Institute of Systems Medicine
|
| Lab |
MaF Lab
|
| Street address |
218 Xinghu Street, B5-527
|
| City |
Suzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
215123 |
| Country |
China |
| |
|
| Platform ID |
GPL25059 |
| Series (1) |
| GSE115093 |
Transcriptome analysis of the treeshrew infected with ZIKV GZ01 |
|
| Relations |
| BioSample |
SAMN09281524 |
| SRA |
SRX4140988 |
