|
| 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 (solidsoftwaretools.com). 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 3â 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 |
| E-mail(s) |
contact@mwschmid.ch
|
| 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 |
|
| Relations |
| SRA |
SRX076053 |
| BioSample |
SAMN00627005 |
