|
| Status |
Public on Dec 01, 2014 |
| Title |
WT_0L_Infection |
| Sample type |
SRA |
| |
|
| Source name |
Source-sink transition leaves
|
| Organism |
Nicotiana attenuata |
| Characteristics |
tissue: leaf
genotype: WT
developmental stage: 35-day-old rossette staged plants
|
| Treatment protocol |
A. alternata infection according to Sun et al. 2014 in Plant Pathology
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Alternaria alternata infection 1 d
|
| Data processing |
Basecalls performed using filter_fq (BGI Internal software)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then transcriptome de novo assembly is carried out with short reads assembling program - Trinity, the parameter is --seqType fq --min_contig_length 100 --min_glue 3 --group_pairs_distance 250 --path_reinforcement_distance 85 --min_kmer_cov 3
Unigene expression difference analysis by Reads Per Kilobase of exon per Megabase of library size (RPKM), and SOAP with parameter -m 0 -x 500 -s 40 -l 35 -v 5 -r 1
|
| |
|
| Submission date |
Sep 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinsong Wu |
| E-mail(s) |
jinsongwu@mail.kib.ac.cn
|
| Organization name |
Kunming institute of Botany, the Chinese Academy of Sciences
|
| Street address |
Lanhei Road 132
|
| City |
Kunming |
| ZIP/Postal code |
650201 |
| Country |
China |
| |
|
| Platform ID |
GPL19212 |
| Series (1) |
| GSE61574 |
Transcriptome analysis of wild tobacco Nicotiana attenuata after Alternaria alternata infection |
|
| Relations |
| BioSample |
SAMN03074606 |
| SRA |
SRX706835 |
