|
| Status |
Public on Apr 24, 2023 |
| Title |
CW_S1 |
| Sample type |
SRA |
| |
|
| Source name |
purple grain wheat
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: grain
age: 30 days after flowering
|
| Growth protocol |
The white grain wheat and purple grain wheat were grown in pots containing a soil: vermiculite mixture (3:1) in a controlled artificial climatic chamber (16 h light/8 h dark photoperiod at 20°C/18 °C).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The stems and buds were collected,and RNA was harvested using Trizol reagent. 5–10 μg total RNA was used as the template for constructing RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Total RNA was isolated and purified using TRIzol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. The RNA integrity was assessed by Bioanalyzer 2100.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase. Then, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.
Cutadapt software was used to remove the reads that contained adaptor contamination. And After removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome (http://www.wheatgenome.org/).
The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM .
Assembly: International Whaet Genome Sequencing Consortium(http://www.wheatgenome.org/)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 12, 2022 |
| Last update date |
Apr 24, 2023 |
| Contact name |
Liu Xiaoting |
| E-mail(s) |
t2775387002@139.com
|
| Phone |
15649857980
|
| Organization name |
Zhengzhou University
|
| Street address |
100 Science Avenue
|
| City |
Zhengzhou |
| ZIP/Postal code |
450001 |
| Country |
China |
| |
|
| Platform ID |
GPL25409 |
| Series (1) |
| GSE198515 |
Integrated Transcriptome and Metabolome Identified Novel Candidate Genes Regulating Anthocyanin Biosynthesis in Colored-Grain Wheat (Triticum aestivum L.) |
|
| Relations |
| BioSample |
SAMN26631453 |
| SRA |
SRX14450310 |
