Difference between revisions of "PSEAE CF.2010"
From Marcotte Lab
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* Table S9. Functional enrichment data for Table S6 | * Table S9. Functional enrichment data for Table S6 | ||
− | == Microarray | + | == Microarray data == |
=== CEL files === | === CEL files === | ||
* http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/GSE21966_CEL.zip | * http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/GSE21966_CEL.zip | ||
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* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.eset_mas5.txt.gz MAS5 pre-processing, ExpressSet] | * [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.eset_mas5.txt.gz MAS5 pre-processing, ExpressSet] | ||
* [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.calls_mas5.txt.gz MAS5 pre-processing, P/M/A calls] | * [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/Huse2010_GSE21966.calls_mas5.txt.gz MAS5 pre-processing, P/M/A calls] | ||
+ | |||
+ | === Probe mapping to PAO1 === | ||
+ | |||
+ | == Genome/Annotation data == | ||
+ | All data were downloaded from http://www.pseudomonas.com on November, 23, 2009. | ||
+ | |||
+ | * ''P. aeruginosa'' PAO1 | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.NC_002516.fna.gz Genomic DNA] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.dna.fasta.gz Transcripts] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.prot.fasta.gz Proteins] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PAO1.PCAP20091123.tsv.gz Annotation(TSV)] | ||
+ | |||
+ | * ''P. aeruginosa'' PA14 | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.NC_008563.fna.gz Genomic DNA] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.dna.fasta.gz Transcripts] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.prot.fasta.gz Proteins] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA14.PCAP20091014.tsv.gz Annotation(TSV)] | ||
+ | |||
+ | * ''P. aeruginosa'' PA7 | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.NC_009656.fna.gz Genomic DNA] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.dna.fasta.gz Transcripts] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.prot.fasta.gz Proteins] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_PA7.PCAP20091123.tsv.gz Annotation(TSV)] | ||
+ | |||
+ | * ''P. aeruginosa'' LESB58 | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.NC_011770.fna.gz Genomic DNA] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.dna.fasta.gz Transcripts] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.prot.fasta.gz Proteins] | ||
+ | ** [http://www.marcottelab.org/users/taejoon/PSEAE_CF/PseudoCAP/PSEAE_LESB58.PCAP20091123.tsv.gz Annotation(TSV)] | ||
+ | |||
---- | ---- | ||
[[Category:Publication]] | [[Category:Publication]] |
Revision as of 14:06, 8 September 2010
Web supplement for 'Huse HK, Kwon T, Zlosnik JEA, Speert DP, Marcotte EM, Whiteley M, Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo, mBIO, :in press (2010) PubMed '
Contents |
Supplement Tables
- Table S1. Strains
- Table S2. P. aeruginosa orthologs
- Table S3. Affymetrix microarray annotation
- Table S4. P. aeruginosa annotation
- Table S5. Differentially expressed genes between progenitors
- Table S6. Differentially expressed genes within isogenic groups (compared to each progenitor/first strain).
- Table S7. Differentially expressed genes between isogenic groups.
- Table S8. Functional enrichment data for Table S7
- Table S9. Functional enrichment data for Table S6
Microarray data
CEL files
- http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/GSE21966_CEL.zip
- You can also download it from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21966 (NCBI GEO)
Gzipped TXT files
- RAW data, before pre-processing
- RMA pre-processing, PM corrected
- RMA pre-processing, Quantile normalized
- RMA pre-processing, ExpressSet
- MAS5 pre-processing, ExpressSet
- MAS5 pre-processing, P/M/A calls
Probe mapping to PAO1
Genome/Annotation data
All data were downloaded from http://www.pseudomonas.com on November, 23, 2009.
- P. aeruginosa PAO1
- P. aeruginosa PA14
- P. aeruginosa PA7
- P. aeruginosa LESB58