|
| Status |
Public on Mar 10, 2011 |
| Title |
Col-WTxLer-WT_full-Endosperm |
| Sample type |
SRA |
| |
|
| Source name |
Full endosperm
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
maternal-ecotype: Columbia-0
paternal-ecotype: Landsberg
maternal-genotype: Wild-type
paternal-genotype: Wild-type
tissue: endosperm
|
| Growth protocol |
Seeds were plated on 0.5X Murashige and Skoog salts (Caisson Laboratories, Inc.), Gamborg’s Vitamins (Sigma), and 2% sucrose; stratified at 4ºC for 2 days; grown in continuous light in a growth chamber for 10 days; and then transplanted to soil and grown in greenhouse conditions (16 hr light). For crosses, flowers were emasculated 2 days before pollination. met1-6 (Col-gl ecotype, [Xiao, 2003 #848]) homozygous plants were obtained from a self-pollinated met1-6 heterozygote that had never been homozygous. fie-1 [Ohad, 1999 #490] and dme-2 [Choi, 2002 #755] heterozygous plants were Ler and Col-gl ecotypes, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Seeds at the mid-torpedo stage to early maturation stage (7-9 days after pollination, ecotype Col-0) were dissected in 0.3 M sorbitol, 5 mM MES (pH 5.7) on a slide under a dissecting microscope. At this stage of development, bilaterally active genes are expressed from both maternal and paternal genomes in embryo and endosperm (S1). Embryos were washed to remove contaminating endosperm. Because the Arabidopsis seed coat has considerable tensile strength, it was possible to separate endosperm from the seed coats and extract RNA from endosperm.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
RNA sequencing
|
| Data processing |
76-bp Illumina reads from cDNA libraries were aligned to Col and Ler cDNA scaffolds (TAIR8) using Bowtie (ref), accepting up to three mismatches in an alignment. Reads that aligned to either Col or Ler with fewer mismatches were assigned to that ecotype.
|
| |
|
| Submission date |
Oct 12, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Toshiro Nishimura |
| E-mail(s) |
tnish@berkeley.edu
|
| Phone |
5106429550
|
| Organization name |
University of California at Berkeley
|
| Department |
Plant and Microbial Biology
|
| Lab |
Daniel Zilberman
|
| Street address |
211 Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE24644 |
Extensive imprinted gene expression in Arabidopsis endosperm |
|
| Relations |
| SRA |
SRX028570 |
| BioSample |
SAMN00115755 |
