|
| Status |
Public on Jul 03, 2017 |
| Title |
IST rep 2 MPI |
| Sample type |
SRA |
| |
|
| Source name |
Seedling
|
| Organism |
Zea mays |
| Characteristics |
tissue: inner stem tissue V2 seedling
line: B73
|
| Treatment protocol |
V2 Seedlings were dissected to extract the inner stem tissue: the outer leaves, including sheath, and also exposed leaf blades were removed. Soft husk leaves were obtained after longitudinal section of the husk including ear, removal of the ear tissue as well as the lignified most external husk leaves layers.
|
| Growth protocol |
B73 maize plants were grown till stage V2 (Abendroth et al 2011) or till flowering (ears with emerging silks, before pollination) in greenhouse (16h of light per day, temperature above 22°C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Plant tissues were ground in liquid Nitrogen and total RNA were extracted using TRIzol in combination with Quiagen RNeasy Plant kit.
A total of 500 ng of total RNA was treated with the Ribo-Zero rRNA Removal Kit, Plant Leaf (Epicentre) to specifically remove ribosomal RNAs. RNA-seq libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocol. Quality and quantity was assessed at all steps by capillary electrophoresis (Agilent Bioanalyser and Agilent TapeStation). Illumina Sequencing-by-synthesis libraries were quantified by fluorometry, immobilized and processed onto a flow cell with a cBot (Illumina) followed by sequencing-by-synthesis with TruSeq v3 chemistry on a HiSeq2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
(rRNA depleted)
|
| Data processing |
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering of RNA-seq reads were done using Trimmomatic (Q20).
RNA-seq reads were aligned to the AGPv4 genome assembly using Tophat.
RNA-seq reads were assembled using Cufflink.
Gene expression level calculation and differential expression analysis was done using Cuffdiff.
Note: The strand polarity of the raw data at SRA is reversed.
Genome_build: AGPv4.32
Supplementary_files_format_and_content: Tab-delimited file containing gene expression level (FPKM) and differential expression data from Cuffdiff.
|
| |
|
| Submission date |
Jan 30, 2017 |
| Last update date |
Apr 22, 2020 |
| Contact name |
Maike Stam |
| Organization name |
University of Amsterdam
|
| Department |
Swammerdam Institute for Life Sciences
|
| Street address |
Science Park 904
|
| City |
Amsterdam |
| ZIP/Postal code |
1098XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17628 |
| Series (2) |
| GSE94252 |
Genome-wide gene expression profile in inner stem tissue of V2 seedlings and husks (maize B73) [RNA-Seq] |
| GSE94254 |
Inner stem tissue of V2 seedlings and husks (maize B73) |
|
| Relations |
| BioSample |
SAMN06279486 |
| SRA |
SRX2527287 |
