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Status |
Public on Nov 24, 2021 |
Title |
Roots, Control 2 |
Sample type |
SRA |
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Source name |
Roots
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Organism |
Zea mays |
Characteristics |
treatment: Control 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 |
SAMN17977867 |
SRA |
SRX10124547 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5090992_45755_ID1462_2-2ZANIN_S2.gtf.gz |
14.3 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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