|
| Status |
Public on Nov 20, 2018 |
| Title |
F44pH7 |
| Sample type |
SRA |
| |
|
| Source name |
cell
|
| Organism |
Lactococcus lactis |
| Characteristics |
strain: F44
treated with: none (pH7)
|
| Treatment protocol |
the strains were cultured at 30°C seed medium with pH 4.0 (treatment) for one hour. One samples were cultured at pH 7.0 as the control group
|
| Growth protocol |
Before treatment, the experimental and the control were cultivated in the seed medium and taken at mid-log phase.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of the strains was isolated by using Quick-RNA™ MicroPrepkit (ZYMO, Research, USA) and treated with DNAse I (NEB) as per manufacturer’s instruction.
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 |
| |
|
| Data processing |
CASAVA(v1.8.2) softwares used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using the software Trimmomatic (v0.30), then mapped to F44 whole genome using bowtie (0.12.7).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using the software rsem.
Gene Differentiation Analysis Using the edgeR (V3.4.2) of Bioconductor Package.
Genome_build: F44
Supplementary_files_format_and_content: xls files include RPKM values for each Sample.
|
| |
|
| Submission date |
Nov 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kairen Tian |
| E-mail(s) |
tiankr544@tju.edu.cn
|
| Phone |
18622795197
|
| Organization name |
Tianjin university
|
| Street address |
No. 135, YaGuan Road, JinNan District
|
| City |
TianJin |
| ZIP/Postal code |
300000 |
| Country |
China |
| |
|
| Platform ID |
GPL23427 |
| Series (2) |
| GSE107135 |
Effects of acid stress on gene transcription of L.lactis strain F44 |
| GSE107137 |
Transcriptome analysis of L.lactis F44 and G423: insights into adaptation to acidic environment |
|
| Relations |
| BioSample |
SAMN08045552 |
| SRA |
SRX3408707 |
