Global analysis of dauer gene expression in Caenorhabditis elegans

These are the 94 microarray experiments that are published in the paper: John Wang and Stuart K. Kim. Global analysis of dauer gene expression in Caenorhabditis elegans, Development 2003 130: 1621-1634. There are 94 individual microarray experiments divided into 3 broad experiments. The first experiment is a time course of dauer exit; each time course is labeled as "Dauer MTC#". The second experiment is a time course of L1 development after starvation arrest; each time couse is labeled "L1 MTC#". The final experiment is a comparison of pure dauers (0 hours) versus 12 hours after dauer exit and are labeled "Dauer Adjust". Every time course was repeated 4 times (#N)however for the dauer 4 and 7 hour time points there are only 3 replicates. For instance, all the time points labeled as "Dauer MTC#1" are from the same starting pool of dauer worms that were aliquoted into 10 fractions and analyzed at the time indicated. Every sample is compared to a common reference RNA that is used throughout all the hybridizations. In some cases there is a "-2" after the hour designation; this means the first hybridization failed for some technical reason and thus the second hybridization (same RNA) is reported. Groups of assays that are related as part of a time series. Keywords: time_series_design

RACE_Vidal_elegans

The general scheme for our RACE experiments is shown in the figure. For our 5' RACE experiments we made use of the trans-spliced SL1 and SL2 leader sequences, instead of ligating a universal sequence to 5' of the transcripts. Approximately 70% of all C. elegans mRNAs have a trans-spliced leader sequence. The great majority of these correspond to a 22 base-long sequence known as "SL1," with "SL2" being the next most frequent, making up 15% of the worm's trans-spliced leaders. The use of SL1/SL2, as opposed to the ligation of an arbitrary sequence to the transcripts' 5' ends has the following advantages: i) no additional manipulation of RNA is needed, ii) the presence of SL1 on a mRNA ensures that the mRNA has an intact 5' end and is full length.nnTo generate the RACE fragments, we reverse transcribed total C. elegans RNA (isolated from mix-stage, asynchronously growing N2 worm population) using either dT16 (for 5' RACE) or used our tailed dT primer (for 3' RACE). Nested PCRs were performed to increase sensitivity and specificity. The generated PCR products were then cloned recombinationally and sequenced from the 5' end, generating "RACE Sequence Tags" (or "RSTs").nnThe RSTs included in this searchable database are vector and quality trimmed (SL and poly(A) sequences were not removed from RSTs). In quality trimming, the first sliding window of 20 nt long with an average quality score higher than 15 marks the start of good quality sequences. Likewise, the first sliding window of 20 nt with average quality score lower than 15 marks the end of good quality sequences.