|
| Status |
Public on Jan 14, 2016 |
| Title |
rmr6 Control T7 Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
youngest wrapped leaf
|
| Organism |
Zea mays |
| Characteristics |
genotype: rmr6-1 mutant
treatment: control
timepoint: after 7 additional days of recovery
|
| Treatment protocol |
Stresses were applied for 10 days: control plants (C) were watered with 75% of disposable water at 0.1dS/m salt concentration; drought-stressed plants (D) with 25% of disposable water at 0.1dS/m salt concentration; salinity-stressed plants (S) with 75% of disposable water at 15dS/m salt concentration; drought plus salinity-stressed plants (D+S) with 25% of disposable water at 15dS/m salt concentration
|
| Growth protocol |
Maize plants were grown in greenhouse until V5-V6 leaf stage with normal watering
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen tissue using the Spectrum Plant Total RNA Kit (SIGMA), and subjected to On-Column DNase Digestion (SIGMA). rRNA depletion were carried out with Ribo-Zero™ rRNA Removal Kits (Plant Leaf) from Epicenter.
TruSeq RNA Library Prep Kit for the first replicate, TruSeq Stranded RNA Library Prep Kit for the Rep2+Rep3, sequenced on Illumina HiSeq2000, multiplex level of 4
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
base-calling and demultiplexing with Illumina CASAVA 1.8
adaptor removal with CUTADAPT version 1.2rc2; parameters: -e 0.08 -O 5 -m 35
contaminant rRNA removal with ERNE_FILTER version 1.2
mapping with tophat-2.0.9; 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
RABT assembly and differential expression analysis usign Cufflinks version 2.2.0
FPKM quantification and normalization between all samples with Cuffquant and Cuffnorm
Genome_build: RefGen ZmB73 Assembly AGPv3
Supplementary_files_format_and_content: Tab-delimited matrix with normalized FPKM values for all the samples.
Supplementary_files_format_and_content: Tab-delimited text files include the raw results of differential expression analysis starting from the uploaded RNA-Seq data.
|
| |
|
| Submission date |
Jul 17, 2015 |
| Last update date |
May 15, 2019 |
| 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 |
GPL15463 |
| Series (1) |
| GSE71046 |
Maize (Zea mays) leaf transcriptome analysis under abiotic stress in wild type and RNA Polymerase IV mutant |
|
| Relations |
| BioSample |
SAMN03877121 |
| SRA |
SRX1100146 |
