|
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 |