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| Status |
Public on Jan 19, 2024 |
| Title |
DTT degradome (D) |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Triticum aestivum |
| Characteristics |
time: 2 days' treatment
age: wheat seedlings
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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 20 ug of total RNA were used to prepare Degradome library. The method with some modification. (1) Approximately 150 ng of poly(A)+ RNA was used as input RNA and annealing with Biotinylated Random Primers. (2) Strapavidin capture of RNA fragments through Biotinylated Random Primers. (3)5’ adaptor ligation to to only those RNAs containing 5’-monophosphates. (4) Reverse transcription and PCR (5) Libraries were sequenced using the 5’ adapter only, resulting in the sequencing of the first 36 nucleotides of the inserts that represented the 5’ ends of the original RNAs. And then we performed the single-end sequencing (36 bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.
Degradome-Seq
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
treatment
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| Data processing |
The purified cDNA library was used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina Hiseq 2500 following vendor’s instruction for running the instrument.
Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software following sequencing image analysis by Pipeline Firecrest Module and base-calling by Pipeline Bustard Module.
A Public software package, CleaveLand3.0 was used for analyzing sequencing data generated.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: excel,expression profiles
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| Submission date |
Jan 19, 2021 |
| Last update date |
Jan 19, 2024 |
| Contact name |
Xing Yu |
| E-mail(s) |
chenyong@henau.edu.cn
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| Phone |
15981820468
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| Organization name |
Henan Agricultural University
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| Street address |
95 Wenhua Road
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| City |
zhengzhou |
| State/province |
Henan |
| ZIP/Postal code |
450002 |
| Country |
China |
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| Platform ID |
GPL18862 |
| Series (1) |
| GSE165108 |
Identify targets of miRNAs involved in ER stress in wheat using degradome sequencing |
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| Relations |
| BioSample |
SAMN17383725 |
| SRA |
SRX9897414 |
| 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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