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Sample GSM2609970 Query DataSets for GSM2609970
Status Public on Dec 31, 2017
Title TMU06(AA)_endosperm_sRNA_rep3
Sample type SRA
 
Source name endosperm
Organism Triticum urartu
Characteristics developmental stage: 6 days after pollination
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using miRVana kit (Ambion 1561) and Plant RNA Isolation Aid (Ambion 9690) to be used for RNA libraries and small RNA libraries.
RNA libraries and small RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Description small RNA
Data processing Illumina CASAVA_v1.8.2 software used for basecalling.
Low-quality reads in the raw RNA-seq data were removed using NGSQCToolkit_v2.3
SlSl transcripts were assembled de novo using Trinity; RNA-seq reads of AA (TMU06) were mapped onto the A genome with TopHat, followed by cufflinks and cuffmerge to generate relative complete transcripts for every annotated gene. Orthologous regions between transcripts among A and Sl genomes were identified using BLAST.
The high-quality reads of AA, DD and AADD were mapped onto the A (T. urartu) and D (Ae. tauschii) genomes allowing two mismatches, while the reads of AA, SlSl and SlSlAA were aligned onto orthologous regions extracted from A and Sl transcripts allowing five mismatches, followed by Cufflink, Cuffmerge and Cuffdiff.
Raw small RNA sequence reads were parsed to remove 3’ adapters and collect 18-30-nt reads with cutadapt. Clean sRNA-seq data of AA, DD and AADD were mapped to A genome, D genome, and combined A and D genomes, respectively using bowtie without mismatch. Small RNA sequencing reads from AA, SlSl, SlSlAA and AADD were all mapped onto the A genome. After removing structural RNAs including ribosomal RNAs, transfer RNAs, snoRNAs, and snRNAs, sRNA reads were normalized by library size using the same weight for each matched locus (reads per 10 million reads, RPTM).
Genome_build: T. urartu (A genome, ftp://climb.genomics.cn/pub/10.5524/100001_101000/100050/A/Assembly/) and Ae. tauschii (D genome, ftp://climb.genomics.cn/pub/10.5524/100001_101000/100054/D/Assembly/); orthologous regions extracted from A and Sl genome transcripts
Supplementary_files_format_and_content: fpkm_tracking files were produced by Cuffdiff, and all other files were generated using in-house Perl scripts
 
Submission date May 09, 2017
Last update date May 15, 2019
Contact name Wu Jiao
E-mail(s) jiaowu123@yeah.net
Organization name Nanjing Agricultural University
Street address 1 Weigang Road
City Nanjing
ZIP/Postal code 210095
Country China
 
Platform ID GPL23449
Series (1)
GSE98684 Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids
Relations
BioSample SAMN06765767
BioSample SAMN06925814
SRA SRX2748534

Supplementary file Size Download File type/resource
GSM2609970_TMU06_AA_endosperm_sRNA_rep3_read_count.txt.gz 14.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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