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Open Access Highly Accessed Research article

Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors

Jinjin Jiang1, Yanlin Shao1, Kun Du1, Liping Ran1, Xiaoping Fang2 and Youping Wang1*

Author Affiliations

1 Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China

2 Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China

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BMC Genomics 2013, 14:72  doi:10.1186/1471-2164-14-72

Published: 1 February 2013

Additional files

Additional file 1: S1:

Distribution of total clean tags and distinct clean tags over different tag abundance categories in each DGE library. (A) Distribution of total tags. Numbers in the brackets of indicate the range of copy numbers for a specific category of tags. For example, [2,5] means all the tags in this category has 2 to 5 copies. Numbers in the parentheses show the total tag copy number for all the tags in that category. (B) Distribution of distinct tags. Numbers in the square brackets indicate the range of copy numbers for a specific category of tags. Numbers in the parentheses show the total types of tags in that category.

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Additional file 3: S3:

Mapping results of total tags and distinct tags of species in seven libraries. Normalized tag copy number was calculated by dividing tag counts for each gene with the total number of tags generated for each library and are presented per one million transcripts. PM and 1MM stand for perfect match and 1 miss match, respectively. (A) Mapping of total tags. (B) Mapping of distinct tags.

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Additional file 2: S2:

Summary of tag mapping in DGE analysis for seven libraries.

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Additional file 4: S4:

List of all genes identified by DGE. The first column represents names of the identified genes. Br_sense_raw and Br_antisense_raw mean the number of tags mapped to sense and antisense genes identified in DGE library of B. rapa. Br_sense_norm and Br_antisense_norm mean total times of detected tags per million in DGE library of B. rapa. GO Component, GO Function and GO Process mean the three main categories (cellular component, molecular function and biological process) in the GO classification, respectively.

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Additional file 5: S5:

Sequencing saturation analysis of the seven libraries of B. rapa (Br), B. oleracea (Bo), B. napus-F1 (Bn-F1), B. napus-F2 (Bn-F2), B. napus-F3 (Bn-F3), B. napus-F4 (Bn-F4) and natural B. napus (Bn-N). The number of detected genes was enhanced as the sequencing amount (total tag number) increased.

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Additional file 6: S6:

Distribution of ratio of distinct tag copy number in each pair of the libraries. ‘A’ was the control and ‘B’ was experimental group in ‘A vs. B’.

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Additional file 7: S7:

List of differentially expressed genes in the early generations of resynthesized B. napus. DEGs between pairs of libraries were shown (Br vs. Bn-F1, Bo vs. Bn-F1, Bn-F1 vs. Bn-F2, Bn-F1 vs. Bn-F3, Bn-F1 vs. Bn-F4, Bn-N vs. Bn-F1. ‘A’ was the control and ‘B’ was experimental group in ‘A vs. B’). TPM: transcript copies per million tags. Raw intensity: the total number of tags sequenced for each gene. FDR: false discovery rate. We used FDR < 0.001 and the absolute value of log2Ratio ≤1 as the threshold to judge the significance of gene expression difference. In order to calculate the log2Ratio and FDR, we used TPM value of 0.001 instead of 0 for genes that do not express in one sample.

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Additional file 8: S8:

The top 20 most up-regulated and down-regulated genes between samples (Br vs. Bn-F1, Bo vs. Bn-F1, Bn-F1 vs. Bn-F2, Bn-F1 vs. Bn-F3, Bn-F1 vs. Bn-F4, Bn-N vs. Bn-F1. ‘A’ was the control and ‘B’ was experimental group in ‘A vs. B’). TPM: transcript copies per million tags. This table does not include genes that only expressed in one sample.

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Additional file 9: S9:

Histogram presentation of gene ontology classification of B. rapa (Br), B. oleracea (Bo), B. napus-F1 (Bn-F1), B. napus-F2 (Bn-F2), B. napus-F3 (Bn-F3), B. napus-F4 (Bn-F4) and natural B. napus (Bn-N).

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Additional file 10: S10:

List of pathway enrichment analysis. Pathways with Q value ≤ 0.05 are significantly enriched in DEGs, see red-border region (‘A’ was the control and ‘B’ was experimental group in ‘A vs. B’).

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Additional file 11: S11:

Both union and intersection DEGs used for HCE clustering analysis.

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