GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM737033 Query DataSets for GSM737033
Status Public on Jan 26, 2012
Title AtLerCentralCell_wildtype_1
Sample type SRA
Source name central cells isolated with LAM
Organism Arabidopsis thaliana
Characteristics ecotype: Landsberg erecta
developmental stage: mature female gametophyte
cell type: central cell
Extracted molecule total RNA
Extraction protocol DOI:10.1038/NMETH.1315. In short, mRNA is reverse transcribed to cDNA with poly(T)-primers fused to anchor sequences for PCR amplification. After PCR amplification, cDNA is sheared and amplified again after the ligation of the sequencing adapters.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD System 3.0
Data processing In short: alignment of the reads to the genome, files are TopHat output. Potential sequencing errors were corrected using the SOLiD Accuracy Enhancement Tool ( The corrected reads were aligned to the Arabidopsis thaliana reference genome (TAIR10) using TopHat (version 1.2, DOI:10.1093/bioinformatics/btp120), which is designed to identify previously undescribed splice junctions. To avoid a potential underestimation of expression levels of gene family members with similar transcript sequences we allowed up to ten alignments per read. The alignments of those reads were then weighted based on the number of uniquely aligned reads in the neighborhood. We used the total number of hits mapping to the transcripts of a locus as expression value for the locus. Hits mapping to more than one locus (ambiguous hits) were proportionally distributed based on the number of unambiguous hits. Loci with transcripts having less than five hits or no hit located within the 250 bps at the 3’ end were discarded, the others declared as being expressed. [see publication for details]
Submission date Jun 03, 2011
Last update date May 15, 2019
Contact name Marc William Schmid
Organization name MWSchmid GmbH
Street address Hauptstrasse 34
City Glarus
ZIP/Postal code 8750
Country Switzerland
Platform ID GPL10088
Series (1)
GSE29719 mRNA-Seq of central cells from the Arabidopsis thaliana female gametophyte
SRA SRX076053
BioSample SAMN00627005

Supplementary file Size Download File type/resource
GSM737033_CC1_accepted_hits.bam 1023.3 Mb (ftp)(http) BAM
GSM737033_CC1_expression.txt.gz 71.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap