This data analyzes gene expression patterns in Arabidopsis whitening mutants, wn1, with defects in chloroplast development. We found that wn1 was a T-DNA insertion line of Arabidopsis AtPTAC10/PAP3 (At3g48500) and exhibited a lethal, albino-like phenotype in the seedling stages. pTAC10 was known as a component of RNA polymerase complex called plastid-encoded RNA polymerase, PEP, in mature chloroplasts. Because wn1 mutants were lethal, we extracted RNA from cotyledons of 7-day-old seedlings from wn1 mutants and Col-0. RNA seq analysis was commissioned by NICEM in Seoul National University, Korea and transcriptome resequencing was confirmed in Macrogen, Korea. Through analysis, we compared gene expression patterns of wn1 mutant and Col-0 seedlings. Overall design: Total mRNA was extracted shoot parts of Col-0 and whitening mutant seedlings grown in 1/2 MS solid media for 7 days. We extract RNA by using Quiagen Plant RNA extraction kit. Transcriptome analysis was commissioned by NICEM Genome Analysis Center in Seoul National University, Korea. We commissioned Macrogen to reanalyze the raw data. Raw data we attached were reanalyzed transcriptome.