GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM3484592

Query DataSets for GSM3484592

Status

Public on Jan 23, 2019

Title

Sample_2-S (SI)

Sample type

SRA

Source name

bronchial aspirate

Organism

Acinetobacter baumannii

Characteristics

tissue: Colistin sensitive A.baumannii

Extracted molecule

total RNA

Extraction protocol

A single colony was used to inoculate 7 ml of BHI liquid culture and incubated at 37 °C for 24h. Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's protocol.
Sequencing libraries were prepared using the Illumina mRNA-seq sample preparation kit following the supplier's instructions except that (a) total RNA was not fragmented and (b) double-stranded cDNA was size-selected (100 to 400 bp) to maximize the recovery of small RNAs. The prepared libraries were evaluated with the High sensitivity D1000 screen Tape (Agilent Tape Station 2200). The indexed libraries were quantified in triplicates with the ABI7900 qPCR instrument using the KAPA Library Quantification Kit, according to the manufacturer’s protocol (KapaBiosystems, Woburn, MA, USA). Five μL of the pooled library at a final concentration of 4 nM were used for sequencing using Illumina Miseq with a A single end stranded library with reads of 50bp. After sequence data generation, raw reads were processed using FastQC v0.11.2 to assess data quality. Reads were then trimmed using Trimmomatic v.0.33.2 to remove sequencing adapters for Single End reads, requiring a minimum base quality of 15 (Phred scale) and a minimum read length of 15 nucleotides. Only trimmed reads were included into downstream analysis.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina MiSeq

Description

SI_2R-2S vs ATCC.xlsx
SI_2R-2S vs ACICU.xlsx

Data processing

Basecalls performed using CASAVA version 1.8.2
Raw reads quality has been checked using FastQC v0.11.2
Sequences were trimmed using Trimmomatic 0.32. Minimum base quality 15 over a 4 bases sliding window was required. Only sequences with longer than 36 nucleotide were considered
Sequence mapping and quantification was performed using Rockhopper v2.0.2
Genome_build: Acinetobacter baumannii ATCC17978 and Acinetobacter baumannii ACICU (NC_010611)
Supplementary_files_format_and_content: Excel files derived from Rockhopper include for both the COL-R/COL-S isogenic couple mRNAs: Trancription Start, Translation Start, Translation Stop, Transcription Stop, Strand, Name, Synonym, Product, Raw Counts, Normalized Count, RPKM, Expression, pValue and qValue.

Submission date

Nov 20, 2018

Last update date

Jan 23, 2019

Contact name

Viviana Cafiso

E-mail(s)

[email protected]

Phone

+39 095 4781245

Organization name

University of Catania