|
| Status |
Public on May 07, 2022 |
| Title |
mutant rep1 |
| Sample type |
SRA |
| |
|
| Source name |
thallus
|
| Organism |
Acinetobacter baumannii |
| Characteristics |
strain: LAC-4
genotype: LAC-4 mutant
|
| Growth protocol |
LAC-4 mutant and wild-type strains were cultured in 20ml TSB until OD600=0.6~0.8, and then the bacteria were collected and resuspended in 1ml PBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted from bacteria samples using TRIzol (Invitrogen) and DNA was digested by DNaseI after RNA extraction. A260/A280 was examined with NanodropTM One spectrophotometer (Thermo Fisher Scientific Inc) to determine RNA quality. RNA Integrity was confirmed by 1% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies).
Total RNAs (2 μg) were used for to prepare sequencing library using KC-Total RNA-seq Library Prep Kit for Illumina® (Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Hiseq X 10 sequencer (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
PAL_1
|
| Data processing |
FastQC (version v0.11.5) was used for raw data quality control.
Trimmomatic (version 0.36) was applied to filter out the adaptor and low-quality reads.
Filtered reads were mapped to the Acinetobacter baumannii genome Acinetobacter_baumannii_GCA_000786735.1(ASM78673v1) by STAR (version 2.5.3a) and evaluated by RSeQC (version 2.6).
The reads count for each gene was calculated using featureCounts (Version 1.5.1).
Genome_build: GCA_000786735.1(ASM78673v1)
Supplementary_files_format_and_content: read count
|
| |
|
| Submission date |
May 07, 2021 |
| Last update date |
May 07, 2022 |
| Contact name |
Xi Zeng |
| E-mail(s) |
cpuzengxi@126.com
|
| Organization name |
Army Medical University
|
| Department |
Department of Microbiology and Biochemical Pharmacy
|
| Street address |
Gaotanyan main street NO.30
|
| City |
Chonqing |
| ZIP/Postal code |
400038 |
| Country |
China |
| |
|
| Platform ID |
GPL30101 |
| Series (1) |
| GSE174057 |
Transcriptome of peptidoglycan-associated lipoprotein mutant and wild-type A. baumannii strains |
|
| Relations |
| BioSample |
SAMN19068071 |
| SRA |
SRX10815563 |
