Gene expression ATLAS of Arabidopsis thaliana (accession Columbia) across its lifecycle

Abstract: Arabidopsis thaliana (accession- Columbia) is an important model plant. RNA-Seq based study of 36 gene expression libraries was carried out to explore transcriptional programs operating in different plant parts (seedling, rosette, root, inflorescence, flower, fruit silique, and seed) and developmental stages (2-leaf stage, 6-leaf stage, 12-leaf stage, senescence stage, dry mature and imbibed seed stage). For each tissue type and developmental stage, three individual plants were used as biological replicates.

Organism part: inflorescence, whole plant, seed, root, silique fruit, flower, rosette

Developmental stage: LP.02 two leaves visible stage, IL.00 inflorescence just visible stage, fruit size 30 to 50% stage, LP.12 twelve leaves visible stage, root development stage, fruit size 70% to final stage, LP.06 six leaves visible stage, dry seed stage, flowering stage, seed imbibition stage, sporophyte senescent stage, inflorescence development stage

Organism: Arabidopsis thaliana

Ecotype: Col-0

Genotype: wild type genotype

Age: Samples are from 20-day, 49-day, 39-day, 15-day, 21-day, 9-day, 22-day, 55-day, 26-day, 45-day

Experimental Designs: growth chamber study EFO, development or differentiation design EFO, organism part comparison design EFO

For more description of the data and sample types see the file PRJEB24664_Sample_descriptors.xlsx or visit   or visit https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422/sdrf

Original data was submitted from

EMBL-EBI ArraExpress: https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-6422

NCBI SRA: https://www.ncbi.nlm.nih.gov/bioproject/PRJEB24664

Protocol description:

Name
Type
Description
Hardware

P-MTAB-71349
growth protocol EFO
Seeds were planted in pots containing commercial potting mix with fertilizers. Pots were covered with clear perforated plastic wrap and kept at 4 degrees celsius for 3 days to break the dormancy. After 3 days plants were transferred to the Intellus Ultra growth chamber (Percival Scientific, IA, USA) which was set to temperature 22-23 degrees celsius, light intensity 120-150 micromol/m2sec under the cycle of 16h light and 8h dark. Soil was kept moist by gently spraying with water every 72 hours to maintain humidity to 50-60%. Sampling time point is given in days after germination.

P-MTAB-71350
nucleic acid extraction protocol EFO
Total RNA from frozen samples was extracted as a method described in Filichkin et al., 2010. Total RNA was used to isolate large RNA as per manufacturer's protocol for miRNeasy Mini kits (Qiagen Inc., USA), and RNase-free DNase (Life Technologies Inc., USA).

P-MTAB-71351
nucleic acid library construction protocol EFO
True-Seq kit (Illumina Inc.) was used to prepare RNA-seq libraries, according to the manufacturer’s protocol.

P-MTAB-71352
nucleic acid sequencing protocol EFO
101bp paired-end sequencing of mRNA was performed by using the standard protocols on Illumina HiSeq 3000.
Illumina HiSeq 3000