Interestingly, an analysis of the gene expression profile in unstimulated CH1 cells revealed that PD-1 was also constitutively expressed in these cells (Accession No. E-TABM-360).
HCT116 cell line grown under high and low glucose conditions: accession number GSE31084; HCT116 after stress treatment: accession number GSE3176; HCT116 cell line treated with actinomycin D: with GSE12459, human embryonic diploid and trisomic cells: accession number GSE28076.
Raw sequencing data for the screen are available under NCBI Bioproject PRJNA284536, containing the datasets for HAP1 gene trap control cells (Accession number SAMN03703230) and cells from the ULBP1 screen (Accession number SAMN03703231).
The microarray data [ 5] are available from the ArrayExpress data repository (http://www.ebi.ac.uk/arrayexpress): human fibrotic liver E-MEXP-2589 E-MEXP-2589 E-MEXP-2589el day-7 (E-MEXP-2583), plastic-activated LI90 cells (Accession No. E-MEXP-2582), and plastic-activated LX-2 cells (E-MEXP-2584).
Lidberg and colleagues previously identified the carboxyl ester lipase-like gene (CELL, genbank accession number M94580) with high homology to the BSSL gene [36].
CENP-A ChIP-Seq data from the PDNC-4 neocentromere cell line (Accession #GSE44724) was processed as previously described (Hasson et al., 2013).
Retroviral vectors encoding human Hyal1, human Hyal2, mouse Hyal2 cloned from NIH 3T3 cells, and rat Hyal2 cloned from 208F rat cells (GenBank accession numbers U03056, U09577, AF535140, and AF535141, respectively) were made by insertion of the cDNAs into the LXSN vector [ 29] and by generation of stable PT67 retrovirus packaging cell lines that produce the vectors as described [ 3, 15, 29].
To validate further our methods of data analysis and to determine whether microarray data from gross heterogeneous tissue are comparable to data generated from LCD epithelial cells, we analyzed independent data sets of LCD epithelial cells (GEO Accession: GDS1439) from benign, localized and metastatic prostate cancer.
In Tyk2 mutant cells, however, only 2297 genes (30%) were influenced by LPS, suggesting that Tyk2-/ cells respond overall much less to LPS than Wt cells (GEO accession number GSE19733).
We have previously identified two antigens 543 and 174 amino acids long, Tp1 and Tp2 respectively, that are recognised by bovine CD8+ T cells (GenBank accession nos. XP_762973 and XP_765583).
