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Sample GSM1377369 Query DataSets for GSM1377369
Status Public on Nov 11, 2014
Title dcl 234 nrpd1 PolyA- RNAseq rep2
Sample type SRA
 
Source name dcl 234 nrpd1 PolyA- RNAseq
Organism Arabidopsis thaliana
Characteristics genotype/variation: dcl 234 nrpd1
tissue: unopened flower buds
molecule subtype: rRNA-depleted Poly A- RNA
Growth protocol Plants were grown with 16hr of light
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description PolyA- RNAseq
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).
 
Submission date Apr 30, 2014
Last update date May 15, 2019
Contact name shaofang Li
Organization name Beijing Academy of Agriculture and Forestry Science
Department Beijing Vegetable Research Center
Street address No 50, ZhanghuaLu, HAIDIAN
City Beijing
State/province Beijing
ZIP/Postal code 100097
Country China
 
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
Relations
BioSample SAMN02741720
SRA SRX530084

Supplementary file Size Download File type/resource
GSM1377369_dcl234nrpd1AM_2_RNA.WIG.gz 39.6 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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