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Sample GSM5285309 Query DataSets for GSM5285309
Status Public on May 07, 2022
Title control rep3
Sample type SRA
 
Source name thallus
Organism Acinetobacter baumannii
Characteristics strain: LAC-4
genotype: wildtype
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 WT_3
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 SAMN19068072
SRA SRX10815562

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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