|
| Status |
Public on Aug 29, 2020 |
| Title |
TAM111_Heading_Dry_rep1 (tamu5) |
| Sample type |
SRA |
| |
|
| Source name |
Flag Leaf
|
| Organism |
Triticum aestivum |
| Characteristics |
developmental stage: Heading
treatment: Dry
cultivar: TAM111
tissue: Flag Leaf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Flag leaf tissues from primary tillers of four individual plants in each replicate were collected and pooled as one sample at each stage of heading (HD) (79 days after transplanting) and grain filling (GF) (100 days after transplanting). Leaf samples were immediately put into liquid nitrogen after their harvest and then stored at -80 ˚C for processing. RNA was extracted using a Qiagen-RNeasy Mini kit according to instruction provided by the manufacturer.
For preparing sequencing libraries, the TruSeq RNA Sample Preparation kit v2 was used following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
TAM111_Heading_Dry_rep1
|
| Data processing |
Illumina BCL2fastq v1.7 was used for basecalling.
Raw reads were filtered by removing adapters and trimming low quality bases (Phred score < 20) at the end of reads using Trimmomatic v0.38 (Bolger et al. 2014). The wheat genome RefSeq v1.0 assembly and gene model annotation files were downloaded from the International Wheat Genome Sequencing Consortium (IWGSC) website (https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Assemblies/v1.0/) (IWGSC 2014).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The filtered reads were then aligned to the reference genome using tool TopHat2 (Kim et al. 2013). Transcript assembles were generated using the computer package Cufflinks (Trapnell et al. 2012), and all assembled transcripts were further merged through the tool Cuffmerge using the wheat reference gene annotation as a guide. The tool Cuffdiff that was included in the Cufflinks package was then used to calculate gene expression level and normalize transcripts abundance to FPKM value (Fragment per kilobase of transcript per million reads mapped) and then make calls of differentially expressed genes (DEGs). The significance (P-values) of DEGs were adjusted using the Benjamini and Hochberg multiple test correction approach (Benjamini and Hochberg 1995) to control the false discovery rate (FDR), and only the genes with an adjusted P-value < 0.05 (FDR < 0.05) and had a fold change value greater than two (the absolute value of Log2 [expression level under dry/wet] is no less than one) were considered to have significant expression difference.
Genome_build: GCA_900519105.1
|
| |
|
| Submission date |
Aug 28, 2020 |
| Last update date |
Sep 09, 2020 |
| Contact name |
Shuyu Liu |
| Organization name |
Texas A&M University System
|
| Department |
Texas A&M AgriLife Research
|
| Street address |
6500 Amarillo Blvd West
|
| City |
Amarillo |
| State/province |
Texas |
| ZIP/Postal code |
79106 |
| Country |
USA |
| |
|
| Platform ID |
GPL23509 |
| Series (1) |
| GSE157033 |
RNA-seq Analysis Reveals Different Drought Tolerance Mechanisms in Two Broadly Adapted Wheat Cultivars ‘TAM 111’ and ‘TAM 112’ |
|
| Relations |
| BioSample |
SAMN15930229 |
| SRA |
SRX9029053 |
