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| Status |
Public on May 01, 2023 |
| Title |
48h NO Treatment rep2 |
| Sample type |
SRA |
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| Source name |
root
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| Organism |
Zea mays |
| Characteristics |
time point: 48h
group: NO Treatment
replicate: 2
tissue: root
genotype: B73
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| Treatment protocol |
Ten bacterial strains were selected in this study, including Arthrobacter, Chryseobacterium, Flavobacterium, Microbacterium, Pedobacter, Pseudomonas, Duganella, Shewanella, Acinetobacter and Bacillus (Table 1). The bacterial strains were streaked onto R2A agar and grown at room temperature for 2-3 d. A single colony from each strain was picked and inoculated in 5 ml of YPD medium. Liquid cultures of the bacteria were grown with agitation at 28 °C overnight. The overnight culture was then transferred into 50 ml of fresh YPD and incubated at 28 °C with agitation overnight. The OD600nm values were measured using a SPECTRONIC ® 20 GENESYSTM spectrophotometer. The liquid cultures were centrifuged, and the pellets were re-suspended in 25 - 50 ml (depending on OD600nm of each bacterium) of 10% YPD medium to equalize individual bacteria concentration to an OD600nm of 0.5. Equal volumes of each bacterial suspension were pooled together to obtain the bacterial synthetic community that was added to the plant roots.
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| Growth protocol |
Seed of the maize inbred line B73 was surface sterilized with Cl2 gas in fume hood for 6 h. After imbibing in aerated 1 mM CaCl2 overnight, seeds were placed on moistened filter paper in petri dishes to germinate in dark at 28 - 30 °C for 2 - 3 d. After germination, seeds were sown in 6-inch round pots filled with 860 g of calcined clay (Diamond Pro Calcined Clay Drying Agent). The pots with calcined clay were autoclaved for 3 times before planting. All transplanting procedures were performed in a laminar flow hood to prevent introduction of bacteria. To try to maintain a sterile environment, each pot was covered and sealed with a 6-inch sterile transparent plastic saucer. Plants were grown in the greenhouse with a 16/8 h dark/light cycle at 21/18 °C (day/night).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs containing small RNAs were extracted using TRI Reagent (RT 111, Molecular Research Center), and then purified using a quick-RNA microprep kit (R1050, Zymoresearch).
standard library construction protocols for mRNAs and microRNAs.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to human genome using HISAT2
Reads counts for each gene
Assembly: maize B73 reference genome
Supplementary files format and content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts
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| Submission date |
Oct 03, 2022 |
| Last update date |
May 02, 2023 |
| Contact name |
Chi Zhang |
| E-mail(s) |
czhang5@unl.edu
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| Organization name |
University of Nebraska - Lincoln
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| Street address |
1901 Vine Street
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| City |
Lincoln |
| State/province |
NE |
| ZIP/Postal code |
68588 |
| Country |
USA |
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| Platform ID |
GPL20156 |
| Series (1) |
| GSE214656 |
Molecular changes in the maize roots transcriptome due to soil microbes |
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| Relations |
| BioSample |
SAMN31136480 |
| SRA |
SRX17780628 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6613911_s44.txt.gz |
182.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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