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| Status |
Public on Jul 11, 2021 |
| Title |
NZ9000-7.0 |
| Sample type |
SRA |
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| Source name |
strain cells
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| Organism |
Lactococcus lactis |
| Characteristics |
strain: parent strain NZ9000
stress: pH 7
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| Treatment protocol |
The exponential phase cells were subjected to acid stress at pH 4.0 for 4 h.The cells were collected by centrifugation at 8000 * g for 2 min at 4 oC, then washed twice with ice-cold 50mM PBS (pH 7.4). The pellets were fully grinded with liquid nitrogen,
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| Growth protocol |
L. lactis cells were cultured in GM17 medium (M17 broth supplied with 0.5% glucose) at 30 oC without shaking
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNAprep pure Bacteria Kit (TIANGEN, Beijing, China) in accordance with the instructions. Purified RNA was quantified by using NanoDrop ND-2000 (Thermo Scientific™, MA, USA). The RNA samples were stored at -80 oC before transcriptome analysis.
The samples were sent to BGI (Shenzhen, China) for transcriptome sequencing. rRNA removing, mRNA purification and fragmentation, cDNA synthesis, adapter ligation and then PCR amplification were performed to construct the cDNA library. The sample library quality was examined using Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, respectively.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences with SOAPaligner/SOAP2
QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and perform coverage analysis.
If alignment result passes QC, we will proceed with downstream analysis including gene expression. Results of gene expression include gene expression levels and differential expression analysis.
Further, we perform Gene Ontology (GO) enrichment analysis and Pathway enrichment analysis.
Genome_build: Lactococcus lactis subsp. cremoris NZ9000
Supplementary_files_format_and_content: tab-delimited .txt files include RPKM values for each Sample
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| Submission date |
Jul 11, 2018 |
| Last update date |
Jul 11, 2021 |
| Contact name |
ming zheng zhu |
| E-mail(s) |
zm151792@gmail.com
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| Organization name |
Jiangnan University
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| Department |
school of biotechnology
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| Street address |
1800 Lihu Road
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| City |
Wuxi |
| State/province |
Jiangsu |
| ZIP/Postal code |
214122 |
| Country |
China |
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| Platform ID |
GPL23427 |
| Series (1) |
| GSE116952 |
Transcriptome analysis of Lactococcus lactis in response to acid stress |
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| Relations |
| BioSample |
SAMN09643533 |
| SRA |
SRX4381396 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3265136_NZ9000_7.0VSNZ9000_4.0.GeneDiffExp.txt.gz |
216.7 Kb |
(ftp)(http) |
TXT |
| GSM3265136_NZ9000_7.0VSNZ9000_4.0.GeneDiffExpFilter.txt.gz |
16.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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