Table 1.
Characteristics of data generation and data analysis of published genome-wide imprinting datasets in Arabidopsis and maize.
| Wolff 2011 | Gehring 2011 | Hsieh 2011 | Pignatta 2014 | Waters 2011 | Zhang 2011 | Xin 2013 | Waters 2013 | Zhang 2014 | |
|---|---|---|---|---|---|---|---|---|---|
| Organism | Arabidopsis | Arabidopsis | Arabidopsis | Arabidopsis | Maize | Maize | Maize | Maize | Maize |
| Strains | Col-0, Bur-0 | Col-0, Ler | Col-0, Ler | Col-0, Ler, Cvi | B73, Mo17 | B73, Mo17 | B73, Mo17 | B73,Mo17,Ki11,Oh43 | B73, Mo17 |
| Starting Material | whole seeds | dissected endosperm/embryo | dissected endosperm/embryo | dissected endosperm/embryo | dissected endosperm/embryo | dissected endosperm/embryo | whole kernels (0,3,5 DAP)/dissected endosperm (7, 10,15 DAP) | dissected endosperm | dissected endosperm |
| Timepoint | 4 DAP | 6 – 7 DAP | 7- 8 DAP | 6 DAP | 14 DAP | 10 DAP | 0,3,5,7,10,15 DAP | 14 DAP | 12 DAP |
| Biological Replicates per cross | 1 | 1 | 2 | 3 | 1 | 1 | 1 | 1 | 1 |
| Sequencing Platform | Illumina GAII | Illumina GAII | Illumina GAII | Illumina HiSeq | Illumina GAII/HiSeq | Illumina HiSeq | Illumina HiSeq | Illumina HiSeq | Illumina HiSeq |
| Read Length | 36 bp | 50/36 bp | 76 bp | 40/80 bp | 2 × 76 bp | 2 × 100 bp | 2 × 90 bp | 2 × 100/2 × 50 bp | 2 × 100 |
| NCBI SRA study ID | SRP005700 | SRP007424 | SRP003799 | SRP033371 | SRP009313 | SRP011991 | SRP026399 | SRP031872 | SRP011991 |
| Genome annotation | TAIR 8 | TAIR 9 | TAIR 8 | TAIR 10 | B73 AGPv2 | n/a | B73 5b.60 | n/a | B73 (V2) |
| Total number of raw reads (hybrids) | 122 mio | 100 mio | 165 mio | 1,837 mio | 245 mio | 149 mio | 379 mio | 1,969 mio | 154 mio |
| Total Number of SNPs | 569,859 | 347,928 | 402,226 | 384,612 | 1.6 mio | 51,416 exonic | 6.5 mio | 28,195–142,033 exonic | 4.2 mio |
| Mapping | |||||||||
| Mapping software | vmatch | TopHat | Bowtie | Tophat v2.0.8 | GSNAP | bwa | TopHat2 | TopHat | TopHat |
| Number mismatches allowed | 2/36 | n/a | 3/76 | 1/40 | 2/36 | n/a | n/a | 2 | n/a |
| Allele-specific mapping bias | Alignment to Col and Bur pseudoreference (only SNPs) | n/a | Alignment to Col and Ler pseudoreference (only SNPs) | n/a | n/a | Mapping to SNP-masked genes | Mapping to both genomes (reference-guided assembly of Mo17) | Mapping to SNP-masked transcripts (filtered gene set v5b.60) | Mapping to SNP-masked genes |
| Counting and Statistics | |||||||||
| Minimal coverage (allelic reads) | ≥10 (≥30) | ≥15 | n/a | n/a | ≥10 reads assigned to one allele in both hybrids | ≥10 per cross | ≥40 (non-stringent: ≥5 per cross) | ≥10 per cross | n/a |
| Summing Reads across | gene | gene | individual SNPs | gene | gene | gene | |||
| Statistical Test | Binomial | Storer-Kim | Fisher’s exact test | Fisher’s exact test | Chi-Square | Chi-Square | Chi-Square | Chi-Square | Chi-Square |
| Multiple Testing Correction | yes (FDR 5%) | no (p < 0.01) | no (p < 0.001) | yes (FDR 1%) | no (p < 0.01) | no (p < 0.05) | unknown adjustment (p < 0.001) | no (p < 0.05 or p < 0.01) | no (p < 0.05) |
| Allelic bias filtering | n/a | only unique expression | MEGs: maternal score ≥ 4x paternal score; PEGs: paternal score ≥ 1.5x maternal score | MEGs: ≥ 85% maternal reads PEGs: ≥ 50% paternal reads | ≥90% reads from one parent in both reciprocal crosses | ≥83% reads from one parent | MEGs: ≥ 90% maternal reads PEGs: ≥ 70% paternal reads < 6 paternally derived reads at 0 DAP | Moderate MEGs: > 90% maternal reads PEGS: > 60% paternal reads. Strong MEGs/PEGs: > 90% maternal/paternal and p < 0.01 | ≥ 83% reads from one parent (reduced criteria: Chi-Square p < 0.05) |
| Filtering out potentially contaminating transcripts derived from the seed coat | Expression SLR in endosperm ≥ 3x seed coat and SLRs in vegetative tissues < 5 (less strigent criteria for low expressed genes) | MEGs expression in endosperm ≥ 2x higher than in the seed coat | Expression levels in endosperm < 4x than LCM-disected endosperm | Expression levels < 2x higher in the seed coat than embryo or endosperm | n/a | n/a | n/a | B73 expression atlas | n/a |
Abbreviations: DAP, days after pollination; FDR, false discovery rate; LCM, Laser Capture Microdissection; MEG, maternally expressed imprinted gene; PEG, paternally expressed imprinted gene; SNP, single-nucleotide polymorphism; SLR, signal log ratio; SRA, short read archive (http://www.ncbi.nlm.nih.gov/sra).