|
| Status |
Public on Jan 29, 2022 |
| Title |
SM_STG1_T0_4 |
| Sample type |
SRA |
| |
|
| Source name |
aerial root
|
| Organism |
Zea mays |
| Characteristics |
cultivar: Sierra Mixe
tissue: aerial root
Stage: stage 1
treatment: no water
|
| Treatment protocol |
Rain events twice a week to trigger mucilage production. Stage 1 Sierra Mixe aerial roots, stage 2 Sierra Mixe aerial roots, and stage 1 B73 aerial roots were collected before a rain event and then 2 and 24 hours after a rain event. After excision, the roots were individually snap-frozen in liquid nitrogen and then stored.
|
| Growth protocol |
Sierra Mixe and B73 maize growing in a high ceiling room (14/10h light/dark cycles and 25/17º C and 85%/90% relative humidity).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The total RNA present in secreted mucilage was extracted using PureLink® RNA Mini Kit (Ambion) and treated with DNase (Ambion®) following the manufacturer’s instructions. A nanodrop spectrophotometer and Agilent Bioanalyzer’s electrophoresis on-chip were used to check RNA quantity and purity.
Libraries for sequencing were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina®) and sequenced in next-generation sequencing platform HiSeq 2500 system (Illumina®) using the TruSeq SBS Kit v3-HS (pair-end 100).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
SM_STG1_T0_4
|
| Data processing |
Pseudo sequence alignment, Kallisto (Kallisto-0.42.3).
100 bootstraps with four threads.
RStudio was used to run R-package sleuth and perform subsequent differential gene expression analysis.
Transcript abundance - Sleuth (version 0.30.0).
Differentially expressed genes (DEGs) between two groups accessed using a Wald test.
Differentially expressed genes FDR < 0.05.
Cut-off was set to a TPM (transcripts per million) expression value of 1.
Genome_build: Zea_mays.B73_RefGen_v4.cdna
Supplementary_files_format_and_content: Tar archives include abundance.h5 and abundance.tsv files; estimated counts and TPM values for each target transcript.
|
| |
|
| Submission date |
Mar 05, 2021 |
| Last update date |
Jan 29, 2022 |
| Contact name |
Vania Pankievicz |
| E-mail(s) |
vaniacarla@gmail.com, pankievicz@wisc.edu
|
| Phone |
6084712444
|
| Organization name |
University of Wiscosin - Madison
|
| Department |
Bacteriology
|
| Street address |
1550 Linder Dr.
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE168384 |
Nitrogen fixation and mucilage production on maize aerial roots is controlled by aerial root development and border cell functions |
|
| Relations |
| BioSample |
SAMN18172248 |
| SRA |
SRX10247934 |
