Atlas and Time Series RNA-seq Data Sets
By Jinliang Yang, Wenbin Mei, , 0

Some RNA-seq data sets for certain lines collected on different tissues or measured at different developmental stages.

Developmental Atlas of maize

Paired RNA and peptide were collected from 23 tissues of B73 inbred.

  • From Walley et al., 2016.
  • Study description from paper abstract: “We built a large-scale gene expression atlas composed of 62,547 messenger RNAs (mRNAs), 17,862 nonmodified proteins, and 6227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development.”
  • Transcriptome: FPKM, (64 Mb excel file)
  • Non-modified proteome: aNSAF, (43 Mb excel file)
  • Phosphoproteome: Spectral counts of both phosphopeptides and phosphoptroteins, (98 Mb excel file)

RNA-Seq with diverse B73 tissues

FPKM matrices are available from the above paper.

  • From Stelpflug et al., 2015.
  • Study description: Microarray versus RNA-Seq comparative analysis with diverse B73 tissues.
  • SRA Study ID: SRP010680
  • Data Size: 50 Gbp; and 31Gb in size

Dry seeds (0 hour) to hour 72 every six hours

  • From Liu et al., 2013.
  • Study description: To discover the transcriptional dynamics during seed germination we have obtained the time course transcriptomes for embryonic shoot apical meristem (SAM) every six hours, starting from dry seeds to hour 72 (3 days).
  • SRA Study ID: SRP017122
  • Data Size: 1.4 Tbp; and 0.9Tb in size
  • Zea mays subsp. mays strain: White Crystal

Dry seeds (0 hour) to hour 192

  • from Yu et al., 2015.
  • Study description: Using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up- and down-regulation and functional transition during leaf development and inferred sets of strongly co-expressed genes.
  • SRA Study ID: SRP044069
  • Data Size: 0.5 Tbp; and 0.3Tb in size
  • Zea mays subsp. mays strain: White Crystal

embryo (0 to 38 days), endosperm (6 to 38 days) and seed (0 to 28 days) every 2 hours

  • from author.
  • Study description: the expression profile among the development of maize embryo, endosperm and seed
  • SRA Study ID: SRP037559
  • Data Size: 178.99 Gbp; and 112.14 Gb in size
  • Zea mays subsp. mays strain: B73

Unpollinated kernels (0 DAP), kernels at 3 and 5 DAP, and endo- sperms from 7, 10, and 15 DAP were obtained by hand dissection (

  • Study description: we performed high- throughput transcriptome sequencing of whole kernels at 0, 3, and 5 d after pollination (DAP) and endosperms at 7, 10, and 15 DAP, using B73 by Mo17 reciprocal crosses.
  • SRA Study ID: GSE48425
  • Data Size: 65.11 Gbp; and 42.07 Gb in size
  • Zea mays subsp. mays strain: B73xMo17 and Mo17xB73

cell type specific transcritome of endosperm, embryo and kernel


  • Study description: we profiled the mRNAs in five major cell types of the differentiating endosperm and in the embryo and four maternal compartments of the maize (Zea mays) kernel.
  • SRA Study ID: GSE62778
  • Data Size: 53.03 Gbp; and 34.30 Gb in size
  • Zea mays subsp. mays strain: B73

transcriptome of kernel and endosperm 0 to 12 days

  • author.
  • Study description: we profiled all mRNAs in the maize kernel and endosperm at eight successive stages during the first 12 d after pollination.
  • SRA Study ID: GSE54131
  • Zea mays subsp. mays strain: B73