|
| Status |
Public on Dec 31, 2020 |
| Title |
NL7 |
| Sample type |
SRA |
| |
|
| Source name |
Whole transcriptome
|
| Organism |
Zea mays |
| Characteristics |
maize genetic resource: Non-Lancaster (BSSS&unknown source)
tissue: leaf
age: V4 stage
|
| Treatment protocol |
none / lines were compared for differential gene expression between two maize genetic resources, Lancaster and Non-Lancaster
|
| Growth protocol |
46 maize inbred lines were grown in the greenhouse under optimal conditions until reaching V4 stage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gene Jet RNA Purification kit (Thermo Fisher Scientific)
Illumina TruSeq(R) Stranded Total RNA LT with Ribo-Zero Plant was used and rRNA was removed using AMPure XP magnetic beads (Beckman Coulter).
Normalized libraries were pooled together and PE 150bp RNAseq was performed on the Illumina MiSeq platform in the IMGGE using MiSeq Reagent Kit v2 (300cycle) with the standard flow cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Illumina MiSeq Basecalling
FastQC (QC>30), Trimmomatic (version 0.32) to filter out low-quality reads, primers and adapter sequences
Reads were mapped onto Zea mays B73 reference genome v3 (available at https://www.maizegdb.org/) using TopHat (insert size 130, standard deviation 50, maximum intron size 100.000).
Reads were assembled using Cufflinks (version 2.2.1) and the final transcriptome assembly was obtained by Cuffmerge as in Trapnell et al. (2012)
Differential expression between Lancaster and Non-Lancaster maize inbred lines was obtained using CuffDiff (treshold of absolute value of log2 fold change greater than 1)
Genome_build: B73 RefGen_v3
Supplementary_files_format_and_content: CuffDiff gene expression output file
|
| |
|
| Submission date |
Dec 30, 2020 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Dragana Dudić |
| Organization name |
Union Nikola Tesla University
|
| Street address |
Cara Dušana 62-64
|
| City |
Beograd |
| ZIP/Postal code |
11000 |
| Country |
Serbia |
| |
|
| Platform ID |
GPL19255 |
| Series (1) |
| GSE164078 |
Comparative leaf transcriptome analysis of Lancaster vs. Non-Lancaster maize inbred lines revealing genetic background associated cold-responsive genes |
|
| Relations |
| BioSample |
SAMN17187383 |
| SRA |
SRX9759572 |
