|
| Status |
Public on Oct 10, 2015 |
| Title |
lyleaves rep3 |
| Sample type |
SRA |
| |
|
| Source name |
leaves
|
| Organism |
Arabidopsis lyrata |
| Characteristics |
strain: lyrata
tissue: leaves
age: plants after bolting
genotype: wild type
|
| Growth protocol |
A. lyrata: long day at 18 degrees, A. thaliana: standard greenhouse conditions, long day
|
| Extracted molecule |
total RNA |
| Extraction protocol |
invitrap spin plant RNA mini kit, including the additional DNA digestion
Fasteris directional RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
For each library independently reads were mapped to the transcriptome sequence of corresponding organism. We download the sequences of the primary transcript from Phytozome version 8.0, file:”Athaliana_167_TAIR10.transcript_primaryTranscriptOnly.fa” for A . thaliana and “Alyrata_107_transcript_primaryOnly.fa” for A. lyrata. Read mapping was done with SOAPv2 with default parameter values. Reads mapping to more than one transcript or to the mitochondrial or chloroplast transcriptome were discarded. Only reads mapping to the forward strand of the transcript were used for further analysis.
|
| |
|
| Submission date |
Nov 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose M. Muino |
| E-mail(s) |
jose.muino@hu-berlin.de
|
| Organization name |
Humboldt University
|
| Department |
Department of Biology
|
| Street address |
Rhoda-Erdmann-Haus (Haus 22); R 1216 Philippstr. 11-13;
|
| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19447 |
| Series (2) |
| GSE63462 |
Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [RNA-Seq] |
| GSE63464 |
Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor |
|
| Relations |
| BioSample |
SAMN03201443 |
| SRA |
SRX763947 |
