|
| Status |
Public on Jan 01, 2018 |
| Title |
Tlr2+/-_PBS_2 |
| Sample type |
SRA |
| |
|
| Source name |
Tlr2+/-_PBS
|
| Organism |
Danio rerio |
| Characteristics |
line: Tlr2 fish line x ABTL
developmental stage: whole embryos
age: 5 days post fertilization
infection: PBS injection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using TRIzol Reagent (Life Technologies) and purified using RNeasy MinElute Cleanup Kit (Qiagen, the Netherlands). The concentration and quality of RNAs were evaluated by NanoDrop 2000 (Thermo Scientific, the Netherlands).
RNAseq was performed using Illumina Hi-Seq 2500
RNAseq was performed using Illumina Hi-Seq 2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The RNAseq data were mapped on zebrafish genome (GRCz10 version) and tag counts were performed by Bowtie 2 using GeneTiles software (http://www. genetiles. com)
Then, we performed normalization and gene expression analysis using the R package and DESeq2
Genome_build: GRCz10
Supplementary_files_format_and_content: Yang_genes_mapped_27-6-2017_DEseq2.xlsx
|
| |
|
| Submission date |
Aug 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Herman Pieter Spaink |
| E-mail(s) |
h.p.spaink@biology.leidenuniv.nl
|
| Phone |
31715275055
|
| Organization name |
Leiden University
|
| Department |
Institute of Biology
|
| Lab |
Molecular Cell Biology
|
| Street address |
Einsteinweg 55
|
| City |
Leiden |
| ZIP/Postal code |
2333 CC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL18413 |
| Series (1) |
| GSE102766 |
Gene expression profiling of the Tlr2 mutant of zebrafish embryos at 4 days post infection of M. marinum |
|
| Relations |
| BioSample |
SAMN07514536 |
| SRA |
SRX3100805 |
