|
| Status |
Public on Feb 27, 2020 |
| Title |
+NH4_Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
primary root apexes
|
| Organism |
Zea mays |
| Characteristics |
inbred: B73
treatment: NH4
|
| Treatment protocol |
24h of growth in nutrient solution supplemented with 1mM KNO3 or 1mM NH4Cl
|
| Growth protocol |
Maize seeds were germinated on wet filter paper at 25°C in the dark; after three days, seedlings were moved to a controlled environmental chamber in 500 ml tanks containing a nutrient medium (Quaggiotti et al. 2003).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent, followed by DNAse treatment
TruSeq RNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
base-calling and demultiplexing with Illumina CASAVA 1.8
adapter clipping and quality filtering with Trimmomatic 0.33
mapping with tophat-2.0.13; parameters: -N 3 --read-gap-length 3 --read-edit-dist 3 --b2-very-sensitive -i 5 -I 60000 --coverage-search --min-coverage-intron 5 --max-coverage-intron 60000 --min-segment-intron 5 --max-segment-intron 60000 --library-type fr-firststrand
Differential expression analysis usign Cufflinks version 2.2.1 --multi-read-correct, --compatible-hits-norm, --dispersion-method per-condition and --library-norm-method quartile
Genome_build: RefGen ZmB73 Assembly AGPv4
Supplementary_files_format_and_content: tab-delimited matrix with normalized RPKM values for all the samples
|
| |
|
| Submission date |
Dec 11, 2019 |
| Last update date |
Feb 27, 2020 |
| Contact name |
Cristian Forestan |
| E-mail(s) |
cristian.forestan@unibo.it
|
| Organization name |
University of Bologna
|
| Department |
Dipartimento di Scienze e Tecnologie Agro-alimentari (DISTAL)
|
| Street address |
Viale Fanin 44
|
| City |
Bologna |
| State/province |
BO |
| ZIP/Postal code |
40127 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE141860 |
Nitrate and ammonium affect the overall maize response to nitrogen availability by triggering specific and common transcriptional signatures in root |
|
| Relations |
| BioSample |
SAMN13541997 |
| SRA |
SRX7348210 |
