Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1

Siying Ye; Chris Cowled; Cheng-Hon Yap; John Stambas

Gene ontology (GO) and KEGG enrichment. Official gene IDs for transcripts that were 451 differentially modulated following HPAI H5N1 infection with or without apocynin treatment were 452 compiled into three target lists. Statistically significant differentially expressed transcripts were defined 453 as having ≥ 2-fold change with a Benjamini-Hochberg adjusted P value < 0.01. A background list of 454 genes was compiled by retrieving all gene IDs identified from the present HiSeq analysis with FPKM > 455 1. Biological process GO enrichment was performed using GOrilla comparing unranked background 456 and target lists (58) and redundant GO terms were removed using REVIGO (59). The target lists were 457 also subjected to KEGG pathway analysis using a basic KEGG pathway mapper (60). (Table S5 ) were designed to estimate the expression of CEACAM1 467 variants in ATII and A549 cells using iTaq Universal SYBR Green Supermix (BioRad) according to 468 manufacturer's instruction. The absence of nonspecific amplification was confirmed by agarose gel 469 All rights reserved. No reuse allowed without permission.