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| Status |
Public on Oct 22, 2019 |
| Title |
ntp6-1ntp7-1 rep1 |
| Sample type |
SRA |
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| Source name |
ntp6-1ntp7-1_seedilng
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Columbia-0
genotype: ntp6-1ntp7-1
age: 3 weeks
tissue: Seeding
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| Growth protocol |
Plants were grown under long day (16 h light/ 8 h darkness) conditions at 22°C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Arabidopsis seedlings were collected, frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
Total RNAs from 14-day-old seedlings were resolved on a 15% denaturing polyacrylamide gel and RNAs of 40-400 nt were recovered from the gel. The size-fractionated RNAs were ligated to a 3’ adaptor using T4 RNA ligase 2, truncated (NEB). The 3’ adaptor-ligated RNAs were resolved on a 15% denature polyacrylamide gel and RNAs of 60-420 nt were recovered. The size-fractionated RNAs were reverse-transcribed with an RT primer that is complementary to the 3’ adaptor using SuperScript III (Life Technologies), followed by two-step PCR amplification. The cDNA was first amplified with the RT primer and a mixture of pre-miRNA-specific forward primers for 10 cycles and secondly amplified for 16 cycles with the 2nd PCR forward and reverse primers using Phusion DNA polymerase (NEB). The PCR products were resolved on a 12% native polyacrylamide gel, and DNAs of 150-230 bp were recovered from the gel as the pre-miRNA 3’ RACE-seq library. The library was sequenced on Illumina HiSeq3000.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
ntp67a-CTTGTA_S14_L005
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| Data processing |
Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was applied for adapter trimming as well as quality control.
The remaining reads were mapped to the genome with hisat2 allowing 3’ soft clipping (Daehwan et al., 2015).
The reads that mapped to multiple loci were removed. Reads that mapped within 50 bp of annotated pre-miRNAs (miRBase release 21) (Ana and Sam, 2014) were retained.
Genome_build: ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/
Supplementary_files_format_and_content: The map file contains the pre-miRNA alignment information and the non-templated sequence information statistics.
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| Submission date |
Aug 25, 2019 |
| Last update date |
Oct 24, 2019 |
| Contact name |
Jianbo Song |
| E-mail(s) |
[email protected]
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| Phone |
18579059335
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| Organization name |
Jiang Xi Agricultural University
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| Street address |
Department of Biochemistry and Molecular Biology, College of Science, Jiang Xi Agricultural University, Nanchang 330045, China
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| City |
Nanchang |
| State/province |
Jiang Xi |
| ZIP/Postal code |
330045 |
| Country |
China |
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| Platform ID |
GPL21179 |
| Series (1) |
| GSE134124 |
Prevalent cytidylation and uridylation of precursor miRNAs in Arabidopsis |
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| Relations |
| BioSample |
SAMN12633307 |
| SRA |
SRX6757075 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4044275_ntp6-1ntp7-1-1.map.txt.gz |
1005.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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