|
| Status |
Public on Dec 27, 2017 |
| Title |
MYQ-Y2-1 |
| Sample type |
SRA |
| |
|
| Source name |
curdlan-producing phase (normoxia)
|
| Organism |
Agrobacterium sp. ATCC 31749 |
| Characteristics |
strain: ATCC 31749
genotype: wild strain
time: 24h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cell of samples were gathered flash frozen in liquid nitrogen. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Hiseq4000 was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Agrobacterium sp. ATCC 31749 using tophat2.
We used cufflinks to calculate the espression of genes in all samples. Fragments Per Kilobase of exon model per Million mapped reads(FPKM) was used to stand for the espression level
Genome_build: AECL01000000
Supplementary_files_format_and_content: FPKM values of genes in all samples were included in the genes.fpkm.xlsx file
|
| |
|
| Submission date |
Dec 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
王 永远 |
| E-mail(s) |
529974917@qq.com
|
| Phone |
13771099543
|
| Organization name |
江南大学
|
| Street address |
滨湖区蠡湖街道1800号
|
| City |
无锡 |
| State/province |
江苏省 |
| ZIP/Postal code |
214122 |
| Country |
China |
| |
|
| Platform ID |
GPL22859 |
| Series (1) |
| GSE92937 |
Transcriptome analysis of Agrobacterium sp. ATCC 31749 wild strain and ΔfnrN based on RNA-seq |
|
| Relations |
| BioSample |
SAMN06187151 |
| SRA |
SRX2447014 |
