Adjustment method for microarray data generated using two-cycle RNA labeling protocol

Fugui Wang1,*, Rui Chen3,*, Dong Ji1,2, Shunong Bai3, Minping Qian1,2, Minghua Deng1,2

1 Center for Quantitative Biology, Peking University, Beijing, 100871,China
2 School of Mathematical Sciences, Peking University, Beijing,100871, China
3 School of Life Science, Peking University,Beijing, 100871,China
* These authors contributed equally to this work.

Rice Microarray Gene Expression Raw Data

1. Data Set 1: The rice embryos were obtained from the seeds soaked in water for 2-3 days. The third and mature expanded leaves were collected when they had just fully expended. Rice seedlings were harvested when they were 2-3cm in height. The panicles were collected when they were 0.6-4cm in length. Total RNA was isolated separately from rice embryos, the third mature leaves, the fifth mature leaves, seedlings and panicles with TRIzol Reagent from Invitrogen Life Technologies. To obtain microarray data covering almost all genes in rice, total RNA from different samples described above was mixed into a big pool called Pre-amplified mRNA sample (PAM) by almost equal magnitude. Eight subgroups were separated from the purified PAM. The half of them were amplified and labeled by the One-Cycle Eukaryotic Target Labeling Assay from Affymetrix (Santa Clara, CA, USA). The resulting samples were called One-Cycle cRNA samples (OCS). The other half were amplified and labeled by the Two-Cycle Eukaryotic Target Labeling Assay from Affymetrix (Santa Clara, CA, USA). The resulting samples were called Two-Cycle cRNA samples (TCS).
            Data Set 1 (35.3M bytes)

2. Data Set 2: This data set contained microarray data from two different samples, including the third leaf primordium and the third mature leaves of rice. Total RNA was extracted from the two samples. And then each of them was separately amplified by two methods, the One-Cycle Labeling Assay and the Two-Cycle Labeling Assay (Affymetrix, Santa Clara, CA, USA). Two replicates were applied for each Assay. Totally there are 8 hybridization samples for the following microarray experiments.

            Data Set 2 (34.8M bytes)

3. Data Set 3: This data set included 21 slides of Affymetrix microarray. There are 7 different stages from rice, including the third leaf primordium, the third mature leaves, and stamen samples at stage 2, 3, 4, 5 and 6 (Stages are partitioned by the development of Stamen). Biological replicates are applied 3 times for each of them. All the 21 mRNA samples are amplified with Two-Cycle Labeling Assay (Affymetrix, Santa Clara, CA, USA). All experimental procedures strictly followed instructions specified in the Affymetrix GeneChip Expression Analysis Technical Manual.

            Data Set 3 (84.3M bytes)

Corresponding Author:
Minghua Deng