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Sample GSM607730 Query DataSets for GSM607730
Status Public on Mar 10, 2011
Title Ler-WTxCol-met1_Endosperm
Sample type SRA
 
Source name Pure endosperm
Organism Arabidopsis thaliana
Characteristics maternal-ecotype: Landsberg
paternal-ecotype: Columbia-0
maternal-genotype: Wild-type
paternal-genotype: met1 (METHYLTRANSFERASE 1) mutant
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 SRX028572
BioSample SAMN00115757

Supplementary file Size Download File type/resource
GSM607730_Ler-WTxCol-met1_Endosperm_RNA-Seq_cDNA_mapping_imprinting.txt.gz 97.2 Kb (ftp)(http) TXT
GSM607730_ReadMe.txt.gz 442 b (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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