|
| Status |
Public on Jan 21, 2017 |
| Title |
lincRNA11195 mutant Arabidopsis |
| Sample type |
SRA |
| |
|
| Source name |
total RNAs, seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain/ecotype: Col0
genotype/variation: lincRNA11195 mutant
tissue: seedlings
developmental stage: two weeks old
treatment: none
|
| Treatment protocol |
Under ABA treatment for 12 hours.
|
| Growth protocol |
For growing Arabidopsis thaliana, seeds were grown on the half MS media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (ambion) for removing DNA contamination.
Libraries were constructed through applying TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
834193_CK
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Adaptor and low quality sequences were trimmed with trim-galore (v0.3.3, --stringency 6); Clean reads were aligned to reference genomes (TAIR10) using STARv2.5.2a with following parameters: --outSAMstrandField intronMotif --outSAMattributes All --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --seedSearchStartLmax 30.
Raw counts of refrence genes were calculated with function "summarizeOverlaps" in R package "GenomicAlignments"; "edgeR" was used to do differential expression (DE) analysis.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Text file including raw count table for reference genes
|
| |
|
| Submission date |
Dec 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dong Wang |
| E-mail(s) |
dongwang@ncu.edu.cn
|
| Phone |
(86) 15921240757
|
| Organization name |
Nanchang University
|
| Street address |
Hong Gu Tan New Road, No. 999
|
| City |
Nanchang |
| State/province |
JiangXi |
| ZIP/Postal code |
330031 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE92419 |
Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants (II) |
| GSE92444 |
Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in Plants |
|
| Relations |
| BioSample |
SAMN06142640 |
| SRA |
SRX2424760 |
