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| Status |
Public on Dec 15, 2015 |
| Title |
Col-0 mRNA-seq replicate 2 |
| Sample type |
SRA |
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| Source name |
WT_14DAG seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Col-0
genotype/variation: wild type
tissue: 14DAG seedlings
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| Growth protocol |
Arabidopsis thaliana seedling were grown for 14days on MS+1% sucrose plate and harvested for total RNA extraction, from which the mRNA were purified for subsequent mRNAs-seq
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were extracted from 14DAG seedlings with TRIzol Reagent (15596–026; Invitrogen).
Strand-specific RNA-Seq libraries generated by using dUTP method (sample 1 and 2) or according to the Illumina Directional mRNA-Seq library prep v1.5 protocol (sample 3 and 4) and sequenced on Illumina GAII.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
high-throughput profiling of transcriptome in Col-0 (wild type), replicate 2,single end
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| Data processing |
Total RNA was extracted from two-week-old seedlings using TRIzol (Invitrogen) according to the manufacturer’s instructions. RNA quality was monitored using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA was purified using the PolyATtract® mRNA Isolation System (Promega, USA) following the manufacturer’s instructions. Strand-specific RNA-seq libraries generated from the WT and double mutant plants were constructed according dUTP method (replicate 1) or the Illumina Directional mRNA-Seq library prep protocol v1.5 (replicate 2) and sequenced on an Illumina GAII. Replicate 1 is paired ended while replicate 2 is single ended. The RNA-seq reads were aligned to the TAIR10 Arabidopsis Genome using TopHat v2.0 (Trapnell et al., 2009). A summary of reads alignment can be found in supplemental table 4. Only uniquely mapped reads were retained for subsequent analysis. The expression levels for gene models from the TAIR10 Arabidopsis Genome were measured and normalized as reads per kilobase of exon model per million mapped reads (RPKM) (Mortazavi et al., 2008). Next, P-values for each gene were calculated by DEGseq based on the MA-plot-based method with random sampling model (MARS) (Wang et al., 2010). Genes with more than 1.5-fold change and P < 0.01 were regarded as differentially expressed genes. For pathway analysis, the list of differential expressed genes and their corresponding log2 fold-changes were analyzed using MapMan (Thimm et al., 2004). Differentially spliced introns were detected as previously reported (Deng et al., 2010). In brief, Fisher's exact test was performed to identify introns with differential splicing between wild type plants and double mutants using read counts from each intron and its two flanking exons. In total, introns with more than 95% read coverage, intron RPKM greater than 5, and a two-sided P-value less than 0.01 were regarded as differentially spliced introns.
Genome_build: TAIR10 Arabidopsis genome
Supplementary_files_format_and_content: wig files were generated using MACS program
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| Submission date |
Dec 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhe Wu |
| E-mail(s) |
wuzhejake@gmail.com
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| Organization name |
John Innes Centre
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| Street address |
Colney
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| City |
Norwich |
| ZIP/Postal code |
NR4 7UH |
| Country |
United Kingdom |
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| Platform ID |
GPL9302 |
| Series (1) |
| GSE75959 |
mRNA-seq data of 14 days old Arabidopsis seedlings in Col-0 and At rz-1b At rz-1c double mutant |
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| Relations |
| BioSample |
SAMN04334952 |
| SRA |
SRX1479926 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1970978_IGDB_WT.bw |
33.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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