|
Status |
Public on Jul 31, 2018 |
Title |
RNA-Seq of Treeshrew ZIKV-infected PBMC +6dpi, 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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Description |
plus6DPBMC-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 |
SAMN09281543 |
SRA |
SRX4140990 |