|
| Status |
Public on Oct 29, 2013 |
| Title |
edm2-4 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
14-d-old entire seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: edm2-4 mutant
tissue: 14-d-old entire seedlings
|
| Treatment protocol |
no special treatment
|
| Growth protocol |
Seeds are sown on MS media, and then treated at 4C overnight. Afterwards, plates are placed under light for germination and growth for 14 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent from 14-d Arabidopsis leaves, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
The extracted RNA was sent to BGI (Shenzhen, China) for RNA-seq library preparation and whole transcriptome sequencing. Briefly, The total RNA was treated with DNaseI and then subjected for mRNA enrichment. The derived mRNA was used as the template for first strand cDNA synthesis by using oligo dT primer. The adaptor was added to the 5’ end of the first strand cDNA and then the second strand cDNA was synthesized by using the primer pairing to the adaptor. The double strand cDNA was sonicated into 300-500 bp fragments for pair-ended sequencing with HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 2
|
| Data processing |
Clean sequenceing reads of edm2 and wild type samples which filter the adapter and low quality were mapped to TAIR10 genome by TopHat 2.0.6 individually . Up to two mismatchs and maximum intron length is 10kb as the threshold, then the unique mapped reads were choosen for subsequent analysis.
Reads number were counted in 5' part and 3' part respectively for each gene which be separated by intronic TE or long methylation intron(length more than 500bp and methylation ratio more than 20%) ,then the 3'/5' expression ratio was compared in edm2 and wild type to look for the 3' down-regulation genes in edm2.
Significantly different degrees given by fisher's exact test.Genes which FDR value less than 0.05 and expression ratio reduced at least two times in edm2 mutant were choosen as candidate.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph format and normalized by library size
|
| |
|
| Submission date |
Oct 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Lan Yang |
| E-mail(s) |
yanglbio@gmail.com
|
| Organization name |
Institute of Plant Physiol & Ecology, Chinese Academy of Sciences
|
| Street address |
300 Fenglin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE51763 |
Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Patterns [RNA-Seq] |
| GSE51764 |
Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Pattern |
|
| Relations |
| BioSample |
SAMN02384878 |
| SRA |
SRX368805 |
