|
| Status |
Public on Mar 27, 2018 |
| Title |
Mycorrhizaed roots of Medicago truncatula [Mt] biological replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
Mycorrhizaed Medicago roots
|
| Organism |
Rhizophagus irregularis |
| Characteristics |
strain: DAOM197198w
developmental stage: all stages
|
| Extracted molecule |
total RNA |
| Extraction protocol |
plants roots were harvested 7 weeks post innoculation
RNA was isolated using the Qiagen RNeasy mini kit according to manufacturers protocol
RNASeq library was made using TruSeq RNA Sample Prep Kit v2 (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file:
Secretome in different hosts with DESeq results and TPM.xlsx
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence
RNASeq data were then mapped to Rhizophagus irregularis genome (Lin, et al., 2013) with manual corrections for secreted proteins. Mapping was done using CLC genomics workbench 9.5.4
Count tables were analyzed using DESeq2 package in R to find out differential expressed AM fungal secreted proteins in different hosts and developmental stages
Genome_build: Rhizophagus irregularis genome (Lin, et al., 2013) with manual corrections on annotation for some secreted proteins
Supplementary_files_format_and_content: Expression levels were represented using TPM value generated by CLC genomics workbench 9.5.4; differential gene analyses were done using DESeq2 package in R
|
| |
|
| Submission date |
Jun 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tian Zeng |
| Organization name |
Wageningen University
|
| Department |
Plant Sciences
|
| Lab |
Laboratory of Molecular Biology
|
| Street address |
Droevendaalsesteeg 1
|
| City |
Wageningen |
| ZIP/Postal code |
6708PB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19734 |
| Series (1) |
| GSE99655 |
Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis |
|
| Relations |
| BioSample |
SAMN07192983 |
| SRA |
SRX2882474 |
