In order to use the mapping file provided by the MapMan homepage (Zm_GENOME_RELEASE_09, http://mapman.gabipd.org), gene identifiers were converted into transcript identifiers by adding the extension "_T01".
In order to produce 5'-labelled RNA substrates, transcripts were dephosphorylated by adding 1 U of antartic phosphatase (New England Biolab) to 20 pmol of RNA and incubating for 30 min at 37°C in a final volume of 10 µL containing 50 mM Tris-HCl, pH 8.5, 0.1 mM EDTA and 40 U of RNAGuard (Amersham Biosciences).
In order to generate 5'-end-labeled RNA substrate, 50 pmol of purified transcripts were dephosphorylated by adding 1 U of Antartic phosphatase (New England Biolabs) and incubating for 1 h at 37°C in a final volume of 10 µL containing 50 mM Bis-Propane, pH 6.0, 1 mM MgCl2, 0.1 mM ZnCl2 and 40 U of RNAGuard.
The transcript copy number of each receptor gene in wild type was estimated by qRT-PCR and the total receptor gene transcript copy number (Cwt) was obtained by adding the transcript copy number of each receptor gene.
Quantification of total HIV-1 transcripts levels was achieved by adding the values of the 9 kb, 4 kb, and 2 kb signals and normalizing to the GAPDH signal.
The conversion explicitly accounted for the length of each transcript's poly(A) tail by adding a fixed length to each known length.
A total count for each transcript in this database was obtained by adding the counts for its constituent exons.
Our catfish microarray design (28K) builds upon a previous 19K channel catfish array by adding recently sequenced immune transcripts from channel catfish along with 7159 unique sequences from closely related blue catfish.
Effective read counts for genes were obtained by adding counts of all transcripts of this gene.
Serial dilutions were prepared by adding the ≅1000 base transcripts from the E. coli genes araB, entF, fixA, and gnd at a final concentration of 10 μM for each transcript in kidney total RNA.
