Guppy density was estimated using depletion sampling [36].
After ribosomal RNA (rRNA) depletion, samples were then purified using the Agencourt RNAClean XP Kit (Beckman Coulter) according to the Epicentre protocol specifications.
After rRNA depletion, samples were purified using a Qiagen RNeasy MinElute Cleanup Kit according to the instructions outlined by the Epicentre Ribo-Zero™ Magnetic Kit.
For ribosomal RNA depletion, samples were treated with rRNA removal solution from the Ribo-Zero magnetic kit for plant seed/root (Epicentre) following manufacturer's instructions.
After ribosomal RNA (rRNA) depletion, samples were purified using the Agencourt RNAClean XP Kit (Beckman Coulter) according to the Epicentre protocol specifications.
There was a significant difference between the values obtained for [H]AM 580 and [C]sucrose in all brain region and capillary depletion samples (Fig. 6; one-way anova on ranks, P < 0.001, followed by Tukey's test, P < 0.05, for both brain region samples and capillary depletion samples; one degree of freedom).
Cells in before and after bead depletion samples (platelets, leukocytes, and erythrocytes) were counted manually using a hemocytometer (improved Neubauer, Hausser Scientific Co., Harsham, PA, USA) to assess sample recovery and purity.
Finally, we subset what remained by insisting that any given transcript must have an RNAPII peak called over its TSS in at least 2/3 of the RECQL5 depletion samples and at least in one of the Doxycycline samples, this left us with a total of 5,140 unique Ensembl transcripts.
Absence of 28S and 18S peaks in the ribosomal RNA (rRNA) depleted sample confirmed good depletion.
