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| Status |
Public on Jan 23, 2019 |
| Title |
Sample_1-S (TS) |
| Sample type |
SRA |
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| Source name |
bronchial aspirate
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| Organism |
Acinetobacter baumannii |
| Characteristics |
tissue: Colistin sensitive A.baumannii
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted from the samples after 12h of incubation using the NucleoSpin RNA (Macherey-Nagel, Dueren, Germany) kit following manufacturer’s protocol with minor modifications. Bacterial cell pellets were lysed by bead-beating procedure in the presence of 50 μL Buffer RA1. Then 3.5 μL ß-mercaptoethanol were added and the lysate was filtrate through NucleoSpin Filters (violet rings). RNA binding condition was adjusted by adding 350 μL of ethanol (70%) to the lysate and the RNA was then extracted with TRIzol reagent (Invitrogen) according to the manufacturer's protocol. The quality of the total RNA was verified using a 2200 TapeStation RNA Screen Tape device (Agilent, Santa Clara, CA, USA) and its concentration ascertained using an ND-1000 spectrophotometer (NanoDrop, Wilmington, DE). Ribosomal RNA was removed using the Ribo-Zero rRNA Removal Kit (Bacteria) from 2 microgram of Total RNA, and the depleted RNA was used as input in the Illumina TruseqRNA stranded kit without PolyA-enrichment.
The prepared libraries were evaluated with the High sensitivity D1000 screen Tape (Agilent Tape Station 2200). The indexed libraries were quantified with the ABI9700 qPCR instrument using the KAPA Library Quantification Kit in triplicates, according to the manufacturer’s protocol (Kapa Biosystems, Woburn, MA, USA). Five μL of the pooled library at a final concentration of 2 nM were used for sequencing using Illumina Miseq with a 150 Paired end-Read sequencing module.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
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| Description |
TS_1R-1S vs ATCC.xlsx
TS_1R-1S and 2R-2S vs ACICU.xlsx
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| 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.
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| Submission date |
Nov 20, 2018 |
| Last update date |
Jan 23, 2019 |
| Contact name |
Viviana Cafiso |
| E-mail(s) |
[email protected]
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| Phone |
+39 095 4781245
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| Organization name |
University of Catania
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| Department |
Biometec
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| Street address |
Via Santa Sofia,97
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| City |
Catania |
| State/province |
Italy |
| ZIP/Postal code |
95123 |
| Country |
Italy |
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| Platform ID |
GPL19442 |
| Series (1) |
| GSE109951 |
Colistin resistant A. baumannii: genomic and transcriptomic traits acquired under colistin therapy |
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| Relations |
| BioSample |
SAMN10453389 |
| SRA |
SRX5034534 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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