Difference between revisions of "PSEAE CF.2010"
From Marcotte Lab
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$EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \ | $EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \ | ||
--ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $CDNA_FILE >> $CDNA_MAP_FILE</pre> | --ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $CDNA_FILE >> $CDNA_MAP_FILE</pre> | ||
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+ | * [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.exonerate.gz Exonerate output against PAO1 transcripts] | ||
+ | * [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.probeset.gz ProbeSet - PAO1 gene mapping] | ||
+ | * [http://www.marcottelab.org/users/taejoon/PSEAE_CF/microarray/PSEAE_1.affy_probes.PSEAE_PAO1.PCAP20091123.dna.fasta.probeset_log.gz Log for bad probesets] | ||
== Genome/Annotation data == | == Genome/Annotation data == |
Revision as of 14:13, 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
A shell script to run exonerate:
EXONERATE="/home/taejoon/bin64/exonerate" PROBE_FILE="PSEAE_1.affy_probes.fasta" GENOME_DIR="/home/taejoon/pkgenome.data/PCAP" TARGET_NAME="PSEAE_PAO1.NC_002516.fna" GENOME_FILE="$GENOME_DIR/$TARGET_NAME" GENOME_MAP_FILE=${PROBE_FILE/%fasta/$TARGET_NAME.exonerate} echo "$PROBE_FILE vs. $GENOME_FILE" echo "#PROBE_FILE : $PROBE_FILE" > $GENOME_MAP_FILE echo "#GENOME_FILE : $GENOME_FILE" >> $GENOME_MAP_FILE $EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \ --ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $GENOME_FILE >> $GENOME_MAP_FILE TARGET_NAME="PSEAE_PAO1.PCAP20091123.dna.fasta" CDNA_FILE="$GENOME_DIR/$TARGET_NAME" CDNA_MAP_FILE=${PROBE_FILE/%fasta/$TARGET_NAME.exonerate} echo "$PROBE_FILE vs. $CDNA_FILE" echo "#PROBE_FILE : $PROBE_FILE" > $CDNA_MAP_FILE echo "#CDNA_FILE : $CDNA_FILE" >> $CDNA_MAP_FILE $EXONERATE -m affine:local -Q dna -T dna --showvulgar no --showcigar no --showalignment no \ --ryo "%qi %ti %tS %qab %qae %tab %tae %et %ei %es %em %s %C\n " $PROBE_FILE $CDNA_FILE >> $CDNA_MAP_FILE
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