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| Status |
Public on Nov 24, 2021 |
| Title |
Roots, Urea 3 |
| Sample type |
SRA |
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| Source name |
Roots
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| Organism |
Zea mays |
| Characteristics |
treatment: Urea
tissue: Roots
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| Extracted molecule |
total RNA |
| Extraction protocol |
For each sample, roots of four plants were pooled together and total RNA was isolated. One g of maize tissue was homogenized in liquid nitrogen and total RNA was extracted from approximately 60 mg of powder with the Spectrum Plant Total RNA Kit (Sigma-Aldrich, St Louis, MO, USA) according to the manufacturer’s instructions.
Library preparation was performed following the Illumina protocol TrueSeq 2.0 using 2 μg of total RNA for each sample
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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 |
Alignment using Hisat2 with default parameters against
Differential expression analysis using cuffdiff with default parameters
Genome_build: B73 RefGen 4 (ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_000005005.6_B73_RefGen_v4)
Supplementary_files_format_and_content: GTF file with read counts
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| Submission date |
Feb 18, 2021 |
| Last update date |
Nov 24, 2021 |
| Contact name |
Fabio Marroni |
| Organization name |
Università di Udine
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| Department |
DI4A
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| Street address |
Via delle Scienze 208
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| City |
Udine |
| ZIP/Postal code |
33100 |
| Country |
Italy |
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| Platform ID |
GPL20156 |
| Series (1) |
| GSE167027 |
Transcriptomic and metabolomic profiling of Zea mays fed with urea and ammonium |
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| Relations |
| BioSample |
SAMN17977863 |
| SRA |
SRX10124539 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5090996_45759_ID1462_6-6ZANIN_S6.gtf.gz |
14.4 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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