|
| Status |
Public on Feb 13, 2023 |
| Title |
MSnoAMcyc4.3 |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Lotus japonicus |
| Characteristics |
tissue: root
genotype: cyc4 mutant line
background ecotype: gifu
media: 1/2 MS medium
am presence: -AM
treatment: 1/2| -AM|cyc4
|
| Treatment protocol |
Plants were grown on either 1/2 MS medium or LN (low-nutrient) medium. +AM designated treatments were exposed to Rhizophagus AM fungi prior to root tissue sampling.
|
| Growth protocol |
Plants were grown in sterile conditions in a growth chamber on one of two media types, dependent upon treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A PureLink RNA mini on-column kit with TRIzol with on-column DNAse treatment
The mRNA library was prepped by BGI Genomics Co., Ltd with polyA selection by an oligo dT library
Arabidopsis and lotus samples were multiplexed, pooled and loaded onto a DNBSEQ Technology Platform sequencer, separately by species
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Data processing |
QC metrics were obtained using FastQC and high-quality (Q>30) read pairs were mapped to RefSeq GCF_000188115.4 using HISAT2 with default parameter settings
Aligned reads were assigned genomic features according to Araport11 (arabidopsis) or Gifu v1.2 (lotus) annotations using featureCounts and read abundances quantified at the isoform level with default parameter settings
Raw counts were filtered for zero and low counts (<2) and library normalization was performed using DESeq2 size factor estimates
Assembly: Arabidopsis: TAIR10 INSDC Assembly GCA_000001735.1; Lotus: LotusBase Lotusjaponicus_Gifu_v1.2
Supplementary files format and content: Text files with counts for each sample by gene isoform
|
| |
|
| Submission date |
Feb 13, 2023 |
| Last update date |
Feb 13, 2023 |
| Contact name |
Heike Sederoff |
| E-mail(s) |
hwsedero@ncsu.edu
|
| Organization name |
North Carolina State University
|
| Department |
Plant & Microbial Biology
|
| Lab |
Sederoff Lab
|
| Street address |
851 Main Campus Dr
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695-7612 |
| Country |
USA |
| |
|
| Platform ID |
GPL33123 |
| Series (1) |
| GSE225213 |
Transcriptome analysis of Arabidopsis thaliana and Lotus japonicus exposed to arbuscular mycorrhizae |
|
| Relations |
| BioSample |
SAMN33272616 |
| SRA |
SRX19355087 |
