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Status |
Public on Jan 08, 2023 |
Title |
Shengsimai, 0hour, rep3 |
Sample type |
SRA |
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Source name |
spike
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Organism |
Triticum aestivum |
Characteristics |
cultivar: Shengsimai tissue: spike time: 0 hour
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Extracted molecule |
total RNA |
Extraction protocol |
The plant total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China) according the instructions provided by the manufacturer. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
73-0-3
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Data processing |
Data process analysis was performed using BMKCloud (www.biocloud.net). Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow: FPKM=cDNAFragments/(MappedFragments(Millions)∗TranscriptLength(kb)) Assembly: NCBI Supplementary files format and content: txt
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Submission date |
Jan 06, 2023 |
Last update date |
Jan 08, 2023 |
Contact name |
Cheng Kou |
E-mail(s) |
koucheng7417@outlook.com
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Phone |
+8615290564435
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Organization name |
Northwest A&F University
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Street address |
3 Tai Cheng Road, Yangling District, Xianyang City, Shaanxi Province, China
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City |
Xianyang |
ZIP/Postal code |
712100 |
Country |
China |
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Platform ID |
GPL25409 |
Series (1) |
GSE222342 |
Mapping quantitative trait loci and developing their KASP markers for Pre-harvest Sprouting resistance of Henan wheat varieties in China |
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Relations |
BioSample |
SAMN32618289 |
SRA |
SRX18955872 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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