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Status |
Public on Jan 29, 2022 |
Title |
SM_STG2_T2_3 |
Sample type |
SRA |
|
|
Source name |
aerial root
|
Organism |
Zea mays |
Characteristics |
cultivar: Sierra Mixe tissue: aerial root Stage: stage 2 treatment: 2 hours after rain event
|
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).
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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|
Description |
SM_STG2_T2_3
|
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.
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|
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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 |
SAMN18172233 |
SRA |
SRX10247949 |