NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM889307 Query DataSets for GSM889307
Status Public on Jun 04, 2012
Title DSH_PA14_exp2
Sample type SRA
 
Source name Pseudomonas aeruginoasa PA14 cDNA
Organism Pseudomonas aeruginosa
Characteristics strain: PA14
experiment: 2
size selection: 150-520 nt adapter ligated RNA
Treatment protocol No additional treatments
Growth protocol early stationary phase (A600 of about 2.6) cultures of P. aeruginosa strains PAO1 and PA14 grown at 37°C in 100 ml of Brain Heart Infusion (BHI) rich medium in 500-ml flasks vigorously shaken
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by RNeasy Kits (Qiagen) with modifications to enrich for small RNAs (<200 nt).
20 to 500 nt RNA was selected by PAGE and electroelution. RNA was first tagged at the 3’-end with 5'-monophosphate oligonucleotide adapters starting with three ribonucleotides followed by a sequence of 20 deoxyribonucleotides and terminally protected with an inverted dT.
RNase H-depletion of tRNA and 5S rRNA was performed essentially as described [PMCID 2665243] with some modifications. Size selection (40-520 nt for experiment 1(exp1) and 150-520 for experiment 2 (exp2)) were performed by PAGE/electroelution. cDNA was generated using the SMARTer™ PCR cDNA Synthesis Kit (Clontech).
Amplicon libraries were prepared for 454 pyrosequencing by PCR amplification with primers tailored for 454-sequencing and including Roche Multiplex Identifiers (MID) for “barcoding”. Free primers, were removed and final size selection (130 to 610 nt) performed by PAGE/electroelution.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model 454 GS FLX Titanium
 
Description small RNA profiling
Data processing Adapters were trimmed using custom scripts written in Python. Reads were mapped to reference genomes [PAO1 genome build: NC_002516.1; PA14 genome build: NC_008463.1] using SEGEMEHL with default settings but reporting all equal best hits. WIG files prepared at single base resolution show log(coverage+1) for each genomic base on plus and minus strands of the reference genome sequences.
Genome Build:
DSH_PA14_exp2_plus.wig: NC_008463.1
DSH_PA14_exp2_minus.wig: NC_008463.1
 
Submission date Mar 07, 2012
Last update date May 15, 2019
Contact name David Stephen Horner
E-mail(s) david.horner@unimi.it
Phone +39 02 503 14884
Organization name Università degli Studi di Milano
Department Molecular Biosciences and Biotechnology
Lab Bioinformatics, Evolution and Comparative Genomics
Street address Via Celoria 26
City Milano
State/province MI
ZIP/Postal code 20133
Country Italy
 
Platform ID GPL15322
Series (1)
GSE36340 Comparative Profiling of Pseudomonas aeruginosa Strains Reveals Differential Expression of Novel Unique and Conserved Small RNAs
Relations
SRA SRX127962
BioSample SAMN00809293

Supplementary file Size Download File type/resource
GSM889307_DSH_PA14_exp2_minus.wig.gz 126.3 Kb (ftp)(http) WIG
GSM889307_DSH_PA14_exp2_plus.wig.gz 122.9 Kb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap