R/data-se_soybean_cn_sub.R
se_soybean_cn_sub.RdThis dataset contains normalized RNA-sequencing read counts from soybean cotyledon across three time stages of development. Early stage cotyledons were collected four days after planting and were green but closed. Middle stage cotyledons were collected while green and open, soon after the plant generated its first set of unifoliate leaves. Late stage cotyledons were collected immediately after the initiation of yellowing and shrinking. To save on size, this example dataset was generated by obtaining a random subset of 1 out of 10 genes from the original resource.
data(se_soybean_cn_sub)
(1) A DelayedMatrix with 7,332 rows and 10 variables and 1 row per
gene. Accessible by assay(se_soybean_cn_sub). (2) A List with 1
list element per treatment group combination and 1 row per gene.
Accessible by rowData(se_soybean_cn_sub).
Normalized and subsetted soybean cotyledon SummarizedExperiment object
assay(se_soybean_cn_sub) Structure:
S1.1 early stage replicate 1 normalized read counts
S1.2 early stage replicate 2 normalized read counts
S1.3 early stage replicate 3 normalized read counts
S2.1 middle stage replicate 1 normalized read counts
S2.2 middle stage replicate 2 normalized read counts
S2.3 middle stage replicate 3 normalized read counts
S3.1 late stage replicate 1 normalized read counts
S3.2 late stage replicate 2 normalized read counts
S3.3 late stage replicate 3 normalized read counts
rowData(se_soybean_cn_sub) list element Structure:
ID gene name
logFC log fold change
logCPM log counts per million
LR likelihood ratio
PValue p-value
FDR FDR value
Brown AV, Hudson KA (2015) Developmental profiling of gene expression in soybean trifoliate leaves and cotyledons. BMC Plant Biol 15:169