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Status |
Public on Dec 31, 2017 |
Title |
TMU06(AA)_endosperm_sRNA_rep3 |
Sample type |
SRA |
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Source name |
endosperm
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Organism |
Triticum urartu |
Characteristics |
developmental stage: 6 days after pollination
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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
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Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2000 |
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Description |
small RNA
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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
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Submission date |
May 09, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Wu Jiao |
E-mail(s) |
jiaowu123@yeah.net
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Organization name |
Nanjing Agricultural University
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Street address |
1 Weigang Road
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City |
Nanjing |
ZIP/Postal code |
210095 |
Country |
China |
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Platform ID |
GPL23449 |
Series (1) |
GSE98684 |
Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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