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| Status |
Public on Nov 11, 2014 |
| Title |
nrpd1 smRNAseq rep2 |
| Sample type |
SRA |
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| Source name |
nrpd1 smRNAseq
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| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: nrpd1
tissue: unopened flower buds
molecule subtype: RNA from 15-40nt
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| Growth protocol |
Plants were grown with 16hr of light
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted with trizol, and treated with Dnase I to clean up the genomic DNA contamination
All the libraries were built using True-seq small RNA preparation kits(Illumina) using different RNA input. dsRNA, the Rnase One(Promega) treated rRNA-depleted RNA. RNAseq and RNAseq-DSN , total rRNA-depleted RNA. RNAseq-DSN,the RNAseq libraries were normalized with DSN kit (Evrogen) before sequencing. PolyA+ RNAseq, polyA+ RNA. PolyA- RNAseq, rRNA-depleted polyA- RNA. smRNA, small RNA of size 15-40nt.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
smRNAseq
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| Data processing |
For dsRNAseq, RNAseq, RNAseq-DSN, PolyA+ RNAseq, PolyA- RNAseq, the reads were mapped back twice. Firstly, the nonredundant reads without adapter trimming were mapped perfectly using BWA without mismatches. Secondly, the unmapped reads trimmed off adapter were mapped perfectly using BWA without mismatches again. The reads were joined together. For smRNAseq, the reads trimmed off adapters were mapped perfectly using BWA without mismatches. For the reads that mapped to multiple position, they are counted only at one randomly position.
Genome_build: TAIR10
Supplementary_files_format_and_content: Wiggle format files with normalized read densities for each nucleotide. The normalized reads were calculated as RPM(reads per million). Please note that some wig files contain both positive and negative values associated with a given chromosome position since the libraries contain strand information, and file s are viewable in popular genome browsers (IGV browser).
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| Submission date |
Apr 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
shaofang Li |
| Organization name |
Beijing Academy of Agriculture and Forestry Science
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| Department |
Beijing Vegetable Research Center
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| Street address |
No 50, ZhanghuaLu, HAIDIAN
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100097 |
| Country |
China |
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| Platform ID |
GPL13222 |
| Series (1) |
| GSE57215 |
Detection of Pol IV-dependent transcripts at the genomic scale in Arabidopsis reveals features and regulation of siRNA biogenesis |
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| Relations |
| BioSample |
SAMN02741723 |
| SRA |
SRX530088 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1377373_nrpd1_2_smRNA.WIG.gz |
19.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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