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| Status |
Public on Apr 27, 2020 |
| Title |
rcsBKO_1 |
| Sample type |
SRA |
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| Source name |
Prokaryote_ΔrcsB mutant
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| Organism |
Yersinia enterocolitica |
| Characteristics |
genotype/varition: rcsBKO
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| Growth protocol |
Y. enterocolitica strains were grown at 26℃ in M63 minimal medium (100 mM of KH2PO4; 15 mM of (NH4)2SO4; 1.8 μM of FeSO4; 1.0 mM of MgSO4; 1.0 μg/ml of thiamine; pH 7.0) with glucose (0.2%).
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted from Y. enterocolitica wild-type and ΔrcsB mutant strains grown to the exponential phase in M63 minimal medium with glucose (0.2%) using TRIzol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
rcsBKO_1_S276_L007
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| Data processing |
The raw reads of the FASTQ format were processed using Perl scripts.
The clean reads were obtained by removing the reads containing the adapters, the low-quality reads and the reads containing the poly N. At the same time, the clean data were analyzed for Q20, Q30 and GC content.
The clean reads were aligned with the reference genome using the Bowtie software (http://bowtie-bio.sourceforge.net/index.shtml).
RESM software (http://deweylab.github.io/RSEM/), which comprehensively considers the sequencing depth and length for this count, was used to quantify gene expression levels, yielding transcripts per million reads (TPM).
The DEGseq (http://bioinfo.au.tsinghua.edu.cn/software/degseq) was used to analyze the differential expression between the two samples. The false discovery rate was controlled through adjusting the P values by using the Benjamini and Hochberg method. The significantly differentiated expressed genes (DEGs) were identified with the inclusion criteria of |log2FC|≥1 and P<0.05.
Genome_build: The reference genome and gene annotation files were downloaded from the genome website (https://www.ncbi.nlm.nih.gov/genome/genomes/1041).
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample .
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| Submission date |
Apr 26, 2020 |
| Last update date |
Apr 27, 2020 |
| Contact name |
Jiao Meng |
| E-mail(s) |
jiaomeng123@yeah.net
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| Phone |
15122808773
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| Organization name |
CAU
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| Street address |
17 Tsinghua East Road
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| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
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| Platform ID |
GPL19851 |
| Series (1) |
| GSE149365 |
Transcriptomic analysis reveals the gene expression profiles and cellular functions regulated by the RcsB in Yersinia enterocolitica |
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| Relations |
| BioSample |
SAMN14733001 |
| SRA |
SRX8177736 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4498641_rcsBKO_1.xls.gz |
96.7 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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