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Sample GSM2609957

Query DataSets for GSM2609957

Status

Public on Dec 31, 2017

Title

TLTU(SlSlAA)_endosperm_mRNA_rep2

Sample type

SRA

Source name

endosperm

Organism

Aegilops longissima x Triticum urartu

Characteristics

developmental stage: 6 days after pollination
genotype: Synthetic allotetraploid wheat SlSlAA

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

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Description

mRNA

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