|
| Status |
Public on May 31, 2023 |
| Title |
KD-GmBIR1 H. glycines infected RNA bio rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Root
|
| Organism |
Glycine max |
| Characteristics |
tissue: Root
cell line: Williams 82 soybean
genotype: KD-GmBIR1 overexpression
infection: Heterodera glycines
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot Phenol RNA extraction from soybean root tissue
mRNA library preperation (polyA enrichment) - NoaSeq PE150 (12G raw data per sample)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
KdinfectedR3
|
| Data processing |
Trimmomatic - fastq trimming and pairing
STAR - mapping the reads to a reference genome
Htseq - counting the reads mapped
DEseq2 - the differential expression analysis
Assembly: Gmax_508_v4.0
Supplementary files format and content: HTseqcounts_All contains counts for each sample that correspond to a particular soybean gene ID generated from HTseq
|
| |
|
| Submission date |
Dec 05, 2022 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Tarek Hewezi |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Tennessee
|
| Department |
Plant Sciences
|
| Street address |
2431 Joe Johnson Drive
|
| City |
Knoxville |
| State/province |
TN |
| ZIP/Postal code |
37996 |
| Country |
USA |
| |
|
| Platform ID |
GPL28801 |
| Series (1) |
| GSE220163 |
The soybean immune receptor GmBIR1 regulates host transcriptome, spliceome, and immunity during cyst nematode infection |
|
| Relations |
| BioSample |
SAMN32064358 |
| SRA |
SRX18504877 |
