FIG 2.

Transcriptome-wide hnRNP L RNA interaction profiles obtained in JSL1 T cells. (a) Six biological replicates of JSL1 T cells, representing triplicate samples of resting and PMA-stimulated cells, were subjected to CLIP-seq analysis. Data were processed by a pipeline identical to that used to analyze hnRNP L binding sites in CD4⁺ cells. (b) Nucleotides of each type of transcript feature were enumerated within hnRNP L binding sites for both resting and stimulated conditions. (c and d) Z-scores for the enrichment of hexamers within binding sites in resting (c) and stimulated (d) cells were calculated by comparing observed hexamer frequencies within CLIP-defined hnRNP L binding sites to randomized binding profiles within bound transcripts. (Insets) The top 20 hexamers were aligned to generate sequence logos.