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Jolly ER
Chin CS
Miller S
Bahgat MM
Lim KC
DeRisi J
McKerrow JH

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Chin CS
Miller S
Bahgat MM
Lim KC
DeRisi J
McKerrow JH
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Research

Gene expression patterns during adaptation of a helminth parasite to different environmental niches

Emmitt R Jolly¹ , Chen-Shan Chin¹ , Steve Miller¹ , Mahmoud M Bahgat² , KC Lim¹ , Joseph DeRisi¹ and James H McKerrow¹

¹California Institute for Quantitative Biomedical Research (QB3) of the University of California, San Francisco, 4th Street, San Francisco, CA 94158 USA

²Theraputic Chemistry Department, Infectious Diseases and Immunology Laboratory, the Road to Nobel Project, the National Research Center, Dokki, 12311 Cairo, Egypt

author email corresponding author email

Genome Biology 2007, 8:R65doi:10.1186/gb-2007-8-4-r65


Published:	24 April 2007

Subject areas: Genome studies, Microbiology and parasitology, Development

Additional files

Additional data file 1:

To rule out dye specific effects, we performed dye-switch experiments for stage-specific comparisons. We plotted the log-ratio of the median (Cy5 signal versus Cy3 signal) from one chip verses the other dye-switched chip. Here we use a color scale to represent the density of each data point plotted. Most data points are accumulated at the red regions. If gene expression differences are small or subtle between two stages ((a) sporocyst versus cercariae and (b) adults versus cercariae), we expect their signals would center around the origin and be randomly distributed (red regions). For genes that are highly expressed, the signals would be high in one chip but low on the other chip. The scatter plots show the expected strong negative correlation between the dye-switched chips. The genes in the adult and sporocyst stages that are highly expressed are not artifacts due to the choice of dye.

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Additional data file 2:

Primer sequences used for real-time PCR analysis

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Additional data file 3:

TC names, annotation and relative ratio of sporocyst to cercariae and adult to cercariae are seen in columns A-F in duplicate. The background was removed from all samples manually as described in type II analysis after normalization in NOMAD, and analyzed using Gen Cluster 3.0 where samples were log transformed and screened to exclude samples with a deviation less than 0.6. All ratios are listed as log2 values.

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Additional data file 4:

The data presented are not ratios, but are averages of raw expression data of each stage independently, where 65,367 is the highest value (we consider values <500 as background)

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Additional data file 5:

All 431 genes highly enriched from the clustering analysis shown in Figure 2

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Additional data file 6:

Transcript comparisons are between sporocysts (Sp) and cercariae (Ce), and adult worms (Ad) and cercariae

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Additional data file 7:

All oligonucleotide sequences used for the schistosome array

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Additional data file 8:

Following experiments done within this paper, the TIGR database containing TC sequences was updated and TC names were changed and expanded. Here is a key mapping TC sequences used in this paper to the new database [78].

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