|
| Status |
Public on Mar 31, 2022 |
| Title |
nodules-pooled RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
nodules
|
| Organism |
Medicago sativa |
| Characteristics |
tissue: nodules
developmental stage: 20 week days old plant
genotype: RegenSY27x
|
| Growth protocol |
RegenSY27x alfalfa plants were grown at 22oC and 18oC day/night temperatures with a photoperiod of 16 hours and three replicates of 8-week-old leaf, stem, flower, seedpod, root and nodule tissue harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was extracted from these plants using a Qiagen RNeasy Plant Mini kit according to the manufacturer's instructions, pooled and used to construct libraries
For the RNA-seq, the libraries were validated using a High Sensitivity Chip on the Agilent 2100 Bioanalyzer. The samples were barcoded, multiplexed and sequenced in an Illumina HiSeq 2000 machine using paired-end reads with 150 cycles. The cDNA library preparation and sequencing reactions were conducted in the Biomedical Genomics Center, University of Minnesota.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw fastq reads were quality-filtered with Trimmomatic (BOLGER et al. 2014) and quality-checked with Fastqc(2010) before and after filtering.
Filtered reads were mapped to the medsa.XinJiangDaYe.gnm1assembly (CHEN et al. 2020) that had been modified to include the genomic clone sequence of MsPho2-B4, using Star (DOBIN et al. 2012).
The generated bam files and featureCounts (LIAO et al. 2014) were used to count uniquely aligned read pairs.
Raw feature counts were then TMM-normalized using edgeR package in R
|
| |
|
| Submission date |
Feb 25, 2022 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Shaun J J Curtin |
| E-mail(s) |
shaun.curtin@usda.gov, curti242@umn.edu
|
| Phone |
6126255715
|
| Organization name |
USDA-ARS-PSRU
|
| Department |
Agronomy and Plant Genetics
|
| Street address |
1991 Upper Buford Circle, 411 Borlaug Hall
|
| City |
St Paul |
| State/province |
MN |
| ZIP/Postal code |
55108 |
| Country |
USA |
| |
|
| Platform ID |
GPL17647 |
| Series (2) |
| GSE197479 |
Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate [RNA-seq] |
| GSE197482 |
Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate |
|
| Relations |
| BioSample |
SAMN26264214 |
| SRA |
SRX14293437 |
