Context: Domain: molecular QTL and multi-omics; Dataset: Matched RNA-seq and ATAC-seq from 84 macrophage donors across 4 conditions (naive, IFNg, SL1344 infection, IFNg+SL1344). Dataset includes 35,034 genes and chromatin accessibility peaks with sample metadata.

Question: How many genes show concordant upregulation under threshold 1.5 in RNA expression and promoter chromatin accessibility when comparing IFNg_SL1344 (condition D) to naive (condition A)?
Answer guideline: Answer must be a single numeric value (e.g., 42) with no units or text.
Answer: 16
Source paper: Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

Question: What is the median fold-change enhancement when comparing the primed infection response to the unprimed infection response for protein-coding genes with mean expression > 5? Round to 2 decimal places.
Answer guideline: Answer must be a numeric value rounded to 2 decimal places (e.g., 0.12).
Answer: 0.12
Source paper: Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

Question: Which condition (IFNg, SL1344, or IFNg_SL1344) shows the highest number of condition-specific ATAC peaks (peaks present with mean accessibility > 8 in that condition but mean accessibility < 5 in naive condition)?
Answer guideline: Answer must be a single word: IFNg, SL1344, or IFNg_SL1344.
Answer: IFNg_SL1344
Source paper: Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

Question: What percentage of the top 500 most variable protein-coding genes (by coefficient of variation in RNA expression) also show high promoter variability (CV > 0.25 in ATAC peaks within TSS ±2kb)? Round to 1 decimal place.
Answer guideline: Answer must be a numeric percentage rounded to 1 decimal place (e.g., 12.3).
Answer: 5.6
Source paper: Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

Question: Which donor shows the highest number of donor-specific differentially expressed genes (genes with |log2FC| > 2 in that donor's SL1344 vs naive comparison but |log2FC| < 1 in all other donors)?
Answer guideline: Answer must be a donor ID (e.g., aipt, bima, etc.).
Answer: jorr
Source paper: Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

Question: What are the top 5 gene names of the protein-coding genes with the highest priming enhancement score among genes with mean expression > 6?
Answer guideline: Answer must be a list of gene symbols, for example: ['GENE1', 'GENE2'], case-sensitive.
Answer: CXCL9, HLA-DRA, SUCNR1, CD97, CD74
Source paper: Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

Question: What is/are the RNA log2FC of the gene(s) that shows discordant regulation under threshold 1.0 and -1.0 when comparing IFNg condition to naive?
Answer guideline: Answer must be a single numeric value (e.g., 42) with no units or text.
Answer: -1.02
Source paper: Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

Question: How many protein-coding genes that are upregulated in SL1344 infection (log2FC > 2 vs naive, mean expression > 5) have at least one ATAC peak within 50kb of their TSS that shows strong positive correlation with the gene's expression across all samples?
Answer guideline: Answer must be a single numeric value (e.g., 42) with no units or text.
Answer: 24
Source paper: Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response