 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 30, 2017 |
| Title |
Transcriptom analyses of Arabidopsis altered meritem program1-32 (amp1-32) mutant as well as wild-type Columbia-0 plants via next-generation sequencing (NGS). |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose:The goals of this study are to compare transcriptome of amp1-32 mutant with that of wild-type Columbia-0 plant and to identify genes whose expression are tightly regualted by AMP1 in Arabidopsis.
Methods: mRNA profiles of 3-week-old wild-type Col-0 and amp1-32 mutant plants were generated by deep sequencing, in duplicate, using Illumina HiSeq2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method : TopHat followed by Cufflinks.
Results: Using an optimized data analysis workflow, we mapped about 30~53 million sequence reads per sample to the Arabidopsis genome (TAIR10). From the 2 biological replicates, we detected 135 up-regulated genes, and 36 down-regulated genes, in the amp1-32 mutant plant.
Conclusions: Our study represents the first detailed analysis of transcriptome of amp1 mutant plants, with biologic replicates. Our results show that AMP1 protein had weak, but significant, effects on transcription of genes important for plant development and responses to stresses.
|
| |
|
| Overall design |
mRNA profiles of 3-week-old wild-type Col-0 and amp1-32 mutant were generated by deep sequencing, in duplicate, using Illumina HiSeq2000.
|
| |
|
| Contributor(s) |
Seo RR, Jung HW |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
May 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ho Won Jung |
| E-mail(s) |
hwjung@dau.ac.kr
|
| Phone |
82512007546
|
| Organization name |
Dong-A University
|
| Department |
Molecular Genetics
|
| Lab |
Plant Immunity & Epigenetics
|
| Street address |
37 Nakdong-Daero 550beon-gil, Saha-gu
|
| City |
Busan |
| ZIP/Postal code |
49315 |
| Country |
South Korea |
| |
|
| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
|
| Samples (4)
|
|
| Relations |
| BioProject |
PRJNA322179 |
| SRA |
SRP075422 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE81618_RAW.tar |
5.6 Mb |
(http)(custom) |
TAR (of DIFF, FPKM_TRACKING, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...