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| Status |
Public on Sep 03, 2020 |
| Title |
R3 |
| Sample type |
SRA |
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| Source name |
Seed_low gluten content
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| Organism |
Triticum aestivum |
| Characteristics |
gluten level: R (low)
tissue: seed
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| Treatment protocol |
Strong (G), middle (Z) and weak (R) gluten wheat were used as the experimental material in this study, and were purchased from Henan province Xinxiang academy of agricultural sciences and Henan huang fan qu dishen seeds agricultural science institute
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0.
Approximately 10 μ g of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, using divalent cations, the poly (A) - or poly (A) + RNA fractions were fragmented into small pieces under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to the final cDNA library according to the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp ( ± 50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following of the merchant's recommended protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Using the Illumina paired-end RNA-seq approach
we aligned reads of sample G1, G2, G3,Z1,Z2,Z3,R1,R2 and R3 to the (ftp://ftp.ensemblgenomes.org/pub/plants/release-36/gtf/triticum_aestivum/) Triticum aestivum L. reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: v36
Supplementary_files_format_and_content: text file include RPKM values for each Sample
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| Submission date |
Nov 19, 2018 |
| Last update date |
Sep 03, 2020 |
| Contact name |
Jinshui Wang |
| E-mail(s) |
wangqi20092012@163.com
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| Phone |
18623711280
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| Organization name |
Henan university of technology
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| Street address |
No. 100 Lianhua street
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| City |
Zhengzhou |
| State/province |
Henan |
| ZIP/Postal code |
450001 |
| Country |
China |
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| Platform ID |
GPL23509 |
| Series (1) |
| GSE122699 |
Transcriptome sequencing of strong, middle and weak gluten strength wheat |
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| Relations |
| BioSample |
SAMN10441180 |
| SRA |
SRX5026190 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3478654_R3.gene.fpkm.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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