Journal: Cell

Article Title: A distinct gene module for dysfunction uncoupled from activation in tumor-infiltrating T cells

doi: 10.1016/j.cell.2016.08.052

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-PD-1 (clone: RMP1-30) Biolegend Cat#: 109109 Anti-Tim3 (clone: 5D12) Generated in house N/A Rat anti-IL-2 (clone: JES6-5H4) Biolegend Cat#: 503807 Anti-TNF-α (clone: MP6-XT22), eBioscience Cat#: 117321 Anti-IFN-γ (clone: XMG-1.2) Biolegend Cat# 505829 Mouse anti-Granzyme B (clone: GB11) Biolegend Cat#: 515405 Rat anti-CD8 (clone: 53–6.7) Biolegend Cat# 100731 Chemicals, Peptides, and Recombinant Proteins Zinpyr-1 Santa Cruz Cat#: sc-213182 Fixable viability dye eFluor506 eBioscience Cat#: 65-0866 Gp100 Genscript Cat#: RP20344 Critical Commercial Assays High Sensitivity DNA Kit (Bioanalyzer) Agilent Cat#: 5067-4626 Qubit dsDNA, High Sensitivity 500rxn Thermo Fisher Scientific Cat#: {"type":"entrez-protein","attrs":{"text":"Q32854","term_id":"75280861","term_text":"Q32854"}} Q32854 Nextera XT Sample Preparation Kit Illumina Cat#: FC-131-1096 NextSeq 500 high output kit V2, 75 cycles Illumina Cat#: FC-404-2005 Deposited Data Data files for CD8+ populations, Microarray This paper need to get accession number Data files for bulk RNA sequencing This paper need to get accession number Data files for single-cell RNA sequencing This paper need to get accession number LCMV exhaustion signature ( Doering et al., 2012 ) {"type":"entrez-geo","attrs":{"text":"GSE41867","term_id":"41867"}} GSE41867 CD8 + Ly49 + Treg signature ( Kim et al., 2015 ) {"type":"entrez-geo","attrs":{"text":"GSE73015","term_id":"73015"}} GSE73015 Experimental Models: Cell Lines MC38-OVA Mark Smyth N/A CT26 ATCC Cat#: CRL-2638 B16-F10 ATCC Cat#: CRL-6475 Experimental Models: Organisms/Strains Balb/c Jackson Laboratory Cat#: 000651 C57BL/6 Jackson Laboratory Cat#: 000664 PMEL Jackson Laboratory Cat#: 005023 OTI Jackson Laboratory Cat#: 003831 MT −/− (backcrossed to C57BL/6 in house) Jackson Laboratory Cat#: 002211 Recombinant DNA SMARTER TSO (with LNA, 10 µM)) Exiqon 5’- AAGCAGTGGTATC AACGCAGAGTACr GrG+G-3’ PCR oligonucleotide primer (10 µM) IDT 5’- AAGCAGTGGTATC AACGCAGAGT-3 Reverse Transcription DNA oligonucleotide primer (RNase-free, 100 µM) IDT 5- AAGCAGTGGTATC AACGCAGAGTACT (30)VN-3 Sequence-Based Reagents Gata3 CRISPR guide sequence Designed in house 5’ - GGTATCCTCCGAC CCACCACG Software and Algorithms GenePattern ( Reich et al., 2006 ) http://software.broadinstitute.org/cancer/software/genepattern/ COMBAT ( Johnson et al., 2007 ) http://www.bu.edu/jlab/wp-assets/ComBat/Download.html Bowtie ( Langmead et al., 2009 ) http://bowtie-bio.sourceforge.net/index.shtml RSEM ( Li and Dewey, 2011 ) http://deweylab.github.io/RSEM/ XL-mHG ( Wagner, 2015 ) https://github.com/flocompbio/xlmhg Other Open in a separate window KEY RESOURCES TABLE Distinct gene modules for T cell dysfunction and activation can be uncoupled.

Techniques: Generated, Recombinant, Sample Prep, Microarray, RNA Sequencing Assay, Sequencing, CRISPR, Software

Journal: Scientific Reports

Article Title: Epigenome-wide association study of diabetic chronic kidney disease progression in the Korean population: the KNOW-CKD study

doi: 10.1038/s41598-023-35485-x

Figure Lengend Snippet: DNA methylation analysis by epigenome-wide association study as discovery and pyrosequencing as validation for the progression of chronic kidney disease (CKD) in diabetic CKD patients. Beeswarm and box plots shows the DNA methylation values of two CpG sites. ( A ) The M-values and beta-values of epigenome-wide association study based on EPIC BeadChip for (a), cg02990553 on AGTR1 (b), and cg10297223 on KRT28 . ( B ) The percentage of differentially methylated CpG sites using pyrosequencing were generated for (a), cg02990553 on AGTR1 (b), and cg10297223 on KRT28 .

Article Snippet: The annotation was performed by an Illumina Infinium MethylationEPIC BeadChip (EPIC chip), which is a microarray platform designed to DNA methylation across over 860,000 CpG sites in human genome.

Techniques: DNA Methylation Assay, Methylation, Generated